Identifier Reference Percentage of Taxa Sampled If Known Figure Digitized Molecules Sequenced Genome Fragment Length Method used to Construct Tree Substitution Model assumed Length of Calibration Calibration equivalent Calibration Factor Units of Calibration Conversion to Millions of Years Phylum Number of Species Pybus & Harvey's g External Branch Length CV l Variance in l Total Tree Length (MY) Tree 004_Pinho_etal_2006_MPE "Pinho, C., N. Ferrand, and D. J. Harris. 2006. Reexamination of the Iberian and North African Podarcis (Squamata: Lacertidae) phylogeny based on increased mitochondrial DNA sequencing. Mol. Phylo. Evol. 38:266-273." 100 2 "cytochrome b, 12S rRNA, 16S rRNA, ND4-tRNALEU, and the control region" mtDNA 2425 Maximum Likelihood GTR+I+G 10 0.01 0.001 substitutions/site 0.0115 Chordata 10 -3.126212504 0.076923882 0.15989572 0.00319583 6.804076087 "(muralis:83.1,((((bocagei:32.2,hispanica_1:39.9):12.9,(carbonelli:37.0,hispanica_2:36.7):14.5):18.5,(hispanica:42.5,(vaucheri:53.8,hispanica:51.5):4.7):14.7):7.7,(hispanica_3:52.8,hispanica:64.1):9.0):2.5);" 007_Filardi&Smith_2005_MPE "Filardi, C. E., and C. E. Smith. 2005. Molecular phylogenetics of monarch flycatchers (genus Monarcha) with emphasis on Solomon Island endemics Mol. Phylo. Evol. 37:776-788." 73 2 ND2 & control region mtDNA 1067 Maximum Likelihood 5.5 0.01 0.001818182 substitutions/site 0.0115 Chordata 17 -0.37466977 0.492301599 0.231798169 0.003582026 9.515070121 "(((chrysomela:30.9,leucotis:17.1):21.3,(C_hamlini:32.5,((melanopsis:6.8,frater:8.2):3.9,(cinerascens:11.0,(castaneiventris:6.8,richardsii:3.5):4.0):1.2):16.3):15.3):9.6,(((((infelix:8.4,(guttula:4.4,trivirgatus:2.8):2.6):4.8,(barbatus:13.3,browni:11.7):0.5):5.5,trivirgatus:13.0):19.4,axillaris:43.0):3.8,(mandensis:27.2,verticalis:16.2):22.2):22.1);" 009_Poulakakis_etal_MPE "Poulakakis, N., P. Lymberakis, E. Valakos, E. Zouros, and M. Mylonas. 2005. Phylogenetic relationships and biogeography of Podarcis species from the Balkan Peninsula, by bayesian and maximum likelihood analyses of mitochondrial DNA sequences. Mol. Phylo. Evol. 37:845-857." 53 2 cytB & 16S mtDNA 927 Maximum Likelihood GTR+I+G 1 1 1 Million years 1 Chordata 9 -2.868277636 0.06565011 0.086956522 0.001080205 12.2 "(((taurica:8.6,((milensis:5.8,gaigeae:5.8):1.9,melisellensis:7.7):0.9):1.4,(erhardii1:9.3,(peloponnesiaca:5.2,erhardii2:5.2):4.1):0.7):2.2,(sicula:9.5,muralis:9.5):2.7);" 010_Lecompte_etal_2005_MPE "Lecompte, E., C. Denys and L. Granjon. 2005. Confrontation of morphological and molecular data: The Praomys group (Rodentia, Murinae) as a case of adaptive convergences and morphological stasis. Mol. Phylo. Evol. 37:899-919." 100 5 cytB & IRBP mtDNA & nuDNA 840 Maximum Likelihood GTR+I+G none Chordata 21 -3.863698503 0.270735058 . . . "((M_yemeni:104.1,(M_fumatus:91.7,(S_albocaudata:32.2,M_albipes:32.2):59.6):12.5):7.4,((M_verheyeni:83.7,(M_coucha:49.0,M_erythroleucus:49.0):34.8):24.0,((Heimyscus:100.0,(M_pernanus:92.8,(H_stella:43.4,H_parvus:43.4):49.4):7.0):5.3,((M_verreauxi:73.2,(Zelotomys:48.9,Colomys:48.9):24.2):22.1,(M_verschureni:87.1,((P_petteri:32.3,P_tullbergi:32.3):42.9,((M_derooi:5.0,M_daltoni:5.0):65.1,(P_degraaffi:59.5,P_jacksoni:59.5):10.8):4.6):11.5):8.5):9.8):2.8):3.7);" 011_Donald_etal_2005_MPE "Donald, K. M., M. Kennedy and H. G. Spencer. 2005. The phylogeny and taxonomy of austral monodontine topshells (Mollusca:Gastropoda: Trochidae), inferred from DNA sequences. Mol. Phylo. Evol. 37:474-483." 71 1B "16S, COI & actin" mtDNA & nuDNA 2327 Bayesian GTR+I+G 8.2 0.1 0.012195122 substitutions/site Mollusca 28 0.217012238 0.815500976 . . . "(((((((((D_nigerrima:0,D_crusoeana:1.1):5.7,((D_arida:11.0,D_coracina:15.2):3.1,D_bicaneliculata:7.7):1.9):0.9,D_zelandica:7.6):1.6,(D_samoaensis:4.6,D_radula:8.0):9.9):1.6,D_concamerata:7.5):15.2,((((A_rudis:0.8,A_constricta:0.6):0.9,A_porcata:2.0):5.6,A_brevis:3.8):14.8,A_diminuta:24.5):15.5):7.6,(((M_confusa:4.5,M_labio1:4.4):5.6,M_perplexa:8.0):8.0,(M_canalifera:10.5,M_labio2:8.2):13.5):11.7):13.1,((C_odontis:1.9,C_crinita:0.9):8.0,C_adelaidae:4.8):22.2):11.3,(((((O_impervia:0,O_variegata:1.4):8.6,O_tabularis:6.3):8.0,O_tigrina:5.7):2.3,O_sinensis:4.3):24.6,O_lineatus:21.0):5.8);" 012_Doadrio&Percides_2005_MPE "Doadrio, I., and A. Perdices. 2005. Phylogenetic relationships among the Ibero-African cobitids (Cobitis, Cobitidae) based on cytochrome b sequence data. Mol. Phylo. Evol. 37:484-493." 100 2 cyt b mtDNA 1140 Bayesian GTR+G 2.8 0.05 0.017857143 substitutions/site 0.0115 Chordata 8 -1.214123427 0.216319614 0.019694189 6.46435E-05 63.86597489 "((((((vettonica:11.2,palucida:9.7):0.6,victoriae:10.3):2.0,maroccana:19.0):1.6,paludica:18.8):15.5,calderoni:24.2):8.8,(zanandreai:28.2,bilineata:31.7):14.6);" 013_PerezEman_2005_MPE "Pérez-Emán, J. L. 2005. Molecular phylogenetics and biogeography of the Neotropical redstarts (Myioborus: Aves, Parulidae). Mol Phylo. Evol. 37:511-528." 100 3 "cyt b, ND2, ND3" mtDNA 2535 Bayesian GTR+I+G 84.8 0.1 0.001179245 substitutions/site 0.0115 Chordata 14 -1.491924285 0.555525832 0.242442632 0.004898202 6.9498748 "(((((((M_albifacies:35.0,((M_cardonai:1.9,M_castaneocapillis2:4.6):16.8,M_castaneocapillus1:20.0):8.1):2.0,M_pariae:35.6):5.2,M_flavivertex:36.4):2.5,(M_torquatus:47.5,((M_melanocephalus2:11.5,(M_melanocephalus1:5.6,M_ornatus:5.6):2.0):20.2,M_albifrons:23.7):10.0):1.5):1.9,M_brunniceps:38.6):9.5,M_miniatus:56.9):13.3,M_pictus:68.4);" 014_Skinner_etal_2005_MPE "Skinner, A., S. C. Donnellan, M. N. Hutchinson, and R. G. Hutchinson. 2005. A phylogenetic analysis of Pseudonaja (Hydrophiinae, Elaphidae, Serpentes) based on mitochondrial DNA sequences. Mol. Phylo. Evol. 37:558-571." 100 3 "ND4, tRNA" mtDNA 770 Bayesian GTR+I+G 1.4 0.05 0.035714286 substitutions/site 0.0115 Chordata 9 -1.648584874 0.370102044 0.013338696 2.54173E-05 89.69089746 "(((((((nuchalis:8.1,machalis:9.2):10.6,affinis:11.2):2.2,(nuchalis:5.9,inframacula:4.2):7.7):2.8,texilis:17.4):4.8,ingrami:19.2):12.6,modesta:33.1):4.8,gullatis:19.7);" 016_Arias&Sheppard_2005_MPE "Arias, M. C., and W. S. Sheppard. 2005. Phylogenetic relationships of honey bees (Hymenoptera:Apinae:Apini) inferred from nuclear and mitochondrial DNA sequence data. Mol. Phylo. Evol. 37:25-35." 100 5 ND2 & EF1-alpha mtDNA & nuDNA 752 Neighbor Joining 21.1 0.05 0.002369668 substitutions/site Arthropoda 11 -0.791128414 0.526576324 . . . "(((((((cerana2:4.3,nuluens:8.3):1.2,nigroc:6.0):0.6,cerana1:4.4):2.3,kosche:13.3):11.0,mellif:30.7):4.4,(labor:16.6,(bingha:0.8,dorsat:10.3):20.8):10.2):4.5,(andren:36.9,florea:16.0):9.0);" 017_Wu_etal_2005_MPE "Wu, C., J. Wu, T. D. Bunch, Q. Li, Y. Wang, Y. Zhang. 2005. Molecular phylogenetics and biogeography of Lepus in Eastern Asia based on mitochondrial DNA sequences. Mol. Phylo. Evol. 37:45-61." 100 2 "cyt b, ND4, 12S" mtDNA 2624 Bayesian TrN+I+G 5 0.01 0.002 substitutions/site 0.0115 Chordata 10 -3.018421401 0.201259883 0.25495855 0.008125483 4.00767663 "((comus:19.2,oiostolus:11.1):4.1,(((((((melainus:2.2,mandschuricus:4.5):10.7,yarkdensis:26.6):9.4,timidus2:5.7):15.6,capensis:10.5):2.3,timidus1:10.7):8.1,sinensis:20.4):3.9,hainanus:22.0):2.4);" 018_Bonacum_etal_2005_MPE "Bonacum, J., P. M. O'Grady, M. Kambysellis, and R. DeSalle. 2005. Phylogeny and age of diversification of the Planitibia species group of the Hawaiian Drosophila. Mol. Phylo. Evol. 37:73-82." 100 3 "16S, COII & Adh, Gpdh, Yp1, Yp2" mtDNA & nuDNA Maximum Likelihood GTR+I+G none Arthropoda 17 -0.810458092 0.737020365 . . . "(((((((hanaulae:6.4,ingens:12.1):6.0,((cyrtoloma:4.5,melanocephala:6.5):3.3,obscuripes:6.5):4.4):3.0,neoperkinsi:8.5):9.6,oahuensis:22.5):7.5,((nigribasis:14.7,neopicta:17.8):1.9,substenoptera:17.4):6.4):5.9,(hemipeza:21.7,((silvestris:7.7,heteroneura:3.1):10.2,(differens:8.1,planitibia:4.8):6.1):10.0):12.2):5.8,(picticornis:46.7,setosifrons:47.6):17.9);" 019_McKenna&Farrell_2005_MPE "McKenna, D. D., and B. D. Farrell. 2005. Molecular phylogenetics and evolution of host plant use in the Neotropical rolled leaf 'hispine' beetle genus Cephaloleia (Chevrolat) (Chrysomelidae: Caddidinae). Mol. Phylo. Evol. 37:117-131." 100 3 "COI, COII, cyt b" mtDNA 2088 Maximum Likelihood GTR+I+G 11.1 0.05 0.004504505 substitutions/site 0.0115 Arthropoda 75 -3.666764266 0.724618857 0.140102867 0.000268888 14.86260488 "((((((((((((C_belti2:2.2,C_quadrilineata:4.2):3.9,(C_belti:6.1,C_luctuosa:5.7):5.0):6.5,C_alternans:12.3):4.2,(((C_fulvicollis:0.5,C_immaculata:1.4):0.5,C_adusta:0):14.5,C_instabilis:15.6):2.8):4.2,(((C_marginella:11.5,C_ornatrix:10.2):3.4,C_stenosoma:15.7):4.0,C_bella:18.8):4.2):1.6,C_suaveola:14.2):3.2,(C_apicata:14.2,C_species136:11.8):7.8):4.3,((((C_antennalis:1.1,C_gilvipes:0.6):1.6,C_flava:4.0):5.9,C_lepida:6.0):10.2,C_distincta:17.1):15.6):4.5,((((C_fenestrata:28.8,C_heliconiae:29.3):4.1,(((C_partita:5.2,C_unctula:6.0):6.6,(C_reventazonica:0,C_nigropicta:0):11.5):6.1,C_gratiosa:13.9):7.0):3.7,((C_leucoxantha:0.7,C_championi:1.2):1.5,C_consanguinea:2.8):20.2):3.9,C_erichsonii:28.3):3.0):2.3,(((((((((((C_suturalis:0.9,C_deficiens:2.5):21.1,C_trivittata2:17.7):3.8,(C_histrionica2:10.2,C_histrio:31.2):5.1):5.7,(C_deficiens:17.2,C_histrionica:16.6):8.5):1.6,C_species181:26.7):4.0,C_trivittata:23.0):1.7,((((C_saliei:6.6,C_congener:5.8):5.0,C_pretiosa:12.6):12.1,(C_trimaculata:4.0,C_tetraspilota:5.5):18.4):7.3,C_stevensi:31.8):4.9):4.9,C_sernivittata:17.2):3.0,((((((C_uhmanii:0,C_metallescens:1.0):3.6,C_schmidti:2.7):7.9,(C_fulvolimbata:1.0,C_splendida:0.9):15.4):2.5,C_ruficollis:12.8):2.7,C_sagittifera:26.0):1.1,C_dorsalis:23.0):2.0):4.7,C_species60:29.5):3.2,C_dilaticollis:41.6):3.7):3.5,((((C_placida:0,C_nigircornis:0):2.1,C_mauliki:0.9):6.9,C_erichsonii:7.0):16.0,C_puichella:28.7):5.2):4.3,(((((C_exigua:10.1,D_species175:7.0):14.7,C_lata:28.5):5.8,(P_columica:26.7,I_rufiventre:21.8):6.2):1.6,C_aequilata2:22.4):3.1,(((((C_cyanea:3.2,C_gilvipes:2.1):17.5,C_species114:20.4):9.9,C_species113:33.1):4.2,C_irregularis:19.1):2.0,C_aequilata:26.8):4.9):3.0);" 020_VanRiel_etal_2005_MPE "Van Riel, P., K. Jordaens, N. Van Houtte, A. M. F. Martins, R. Verhagen, and T. Backeljau. 2005. Molecular systematics of the endemic Leptxini (Gastropoda: Pulmonata) on the Azores islands. Mol. Phylo. Evol. 37:132-143." 100 3 "16S, COI & ITS" mtDNA & nuDNA 2612 Maximum Likelihood GTR+I+G 23.5 0.02 0.000851064 substitutions/site Mollusca 10 -0.482092639 0.592160565 . . . "(((LAF:36.7,(LAE:46.2,LAW:36.0):15.0):9.8,LM:36.9):23.5,((HS:18.6,((LD:5.7,LP:5.7):7.7,(LT:5.4,LG:3.0):3.8):7.3):4.3,LC:32.9):21.6);" 021_Allegrucci_etal_2005_MPE "Allegrucci, G., V. Todisco, and V. Sbordoni. 2005. Moleulcar phylogeography of Dolichopoda cave crickets (Orthoptera, Rhaphidophoridae): A scenario suggested by mitochondrial DNA. Mol. PHylo. Evol. 37:153-164." 100 2 COI. 16S mtDNA 1498 Maximum Likelihood GTR+I+G 21.1 0.01 0.000473934 substitutions/site 0.0115 Arthropoda 11 -4.077037699 0.029886686 0.483754315 0.026002026 1.952745452 "(linderi:38.1,((ligustica:43.5,(laetitiae:36.9,geniculata:31.4):4.3):3.9,(capreensis:27.9,palpata:27.9):20.9):1.5,(((baccetti:35.6,aegilion:37.3):2.3,schiavazzi:55.4):1.9,(bormansi:33.6,cymensis:32.7):7.7):10.8);" 022_Shull_etal_2005_MPE "Shull, H. C., M. Pérez-Losada, D. Blair, K. Sewell, E. A. Sinclair, S. Lawler, M. Ponniah, and K. A. Crandall. 2005. Phylogeny and biogeography of the freshwater crayfishy Euastacus (Decapoda: Parastacidae) based on nuclear and mitochondrial DNA. Mol. Phylo. Evol. 37:249-263." 100 3 "COI, 16S, 12S & 28S" mtDNA & nuDNA 2109 Maximum Likelihood TVM+I+G 3 0.01 0.003333333 substitutions/site Arthropoda 44 -4.071366907 0.358601901 . . . "((fleckeri:3.5,robertsi:10.8):35.8,(australasiensis:9.6,(maidae:18.9,(polyselosus:11.0,((garnillaroi:14.2,spinichellsius:7.5):4.4,((hystricosus:1.2,urospinosus:0.0):12.3,sulcatus:14.7):6.0,((clarkae:13.1,suttoni:15.4):1.6,(((vallentulus:0,sulcatus:0):5.8,(dangadi:5.8,gurnar:8.3):2.7):9.2,(mirangudjin:11.0,neohirsutus:10.8):1.5):2.3):1.6):1.4):4.2,(reducius:22.0,(((jagara:14.5,(urospinosus:11.5,setosus:5.3):5.8):1.3,((monteithorum:13.5,eungella:13.1):1.2,(bindal:14.7,(yigara:10.9,balanensis:19.1):6.4):0.8):1.2):3.4,((kershawi:8.2,woiwuru:16.5):3.5,((diversus:12.3,bidawalus:12.5):6.0,((crassus:6.6,rieki:5.2):4.9,((dharawalus:7.0,((brachythorax:5.4,daytoni:4.2):2.0,guwinus:5.0,yanga:4.1):1.2):2.2,(((bispinosus:3.6,yarraensis:2.9):0.4,(armatus:0.7,crassus:0):3.7):4.9,(species:3.9,spinifer:4.1):3.1):2.7):2.5):1.4):2.1):5.5):1.9):1.6):2.1):8.3);" 023_Heinze_etal_2005_MPE "Heinze, J., A. Trindl, B. Seifert, and K. Yamauchi. 2005. Evolution of male morphology in the ant genus Cardiocondyla. Mol. Phylo. Evol. 37:278-288." 87 3 "COII, 16S" mtDNA 1960 Bayesian GTR+I+G 27.1 0.1 0.003690037 substitutions/site 0.0115 Arthropoda 17 0.107533374 1.512424758 0.088605103 0.000523391 22.89189156 "(argenitina:68.0,(minutior:58.8,((((batesii:3.9,nigra:7.3):22.4,(((ulianini:7.0,sahlbergi:5.2):3.5,(elegans:9.8,bulgarica:8.5):4.1):18.4,(koshewnikovi:14.1,stambuloffii:17.7):21.3):3.9):8.5,(atalanta:26.6,(mauritanica:10.2,(kagutsuchi:5.4,strigifrons:5.4):9.1):7.7):17.3):14.5,(emeryi:63.5,(wroughtonii:0.9,obscurior:1.8):57.6):7.5):8.5):10.0);" 025.1_Eberhard_Bermingham_1_MPE "Eberhard, J. R., and E. Bermingham. 2005. Phylogeny and comparative biogeography of Pionopsitta parrots and Pteroglossus toucans. Mol. Phylo. Evol. 36:288-304." 89 3 "ATPase6, ATPase8, COI, cyt b" mtDNA 2168 Maximum Likelihood TIM+I+G 1.163 0.05 0.042992261 substitutions/site 0.0115 Chordata 8 0.761448268 1.579681468 0.126244003 0.002656258 14.60521875 "((((vulturina:0.572,caica:0.546):0.262,(aurantiigena:0.589,barrabandi:0.5):0.644):0.753,((coccinicolaris:0.43,haematotis:0.209):0.543,pulchra:0.978):0.425):2.05,pineata:4.212);" 025.2_Eberhard_Bermingham_2_MPE "Eberhard, J. R., and E. Bermingham. 2005. Phylogeny and comparative biogeography of Pionopsitta parrots and Pteroglossus toucans. Mol. Phylo. Evol. 36:288-304." 100 4 "ATPase6, ATPase8, COI, cyt b" mtDNA 2168 Maximum Likelihood TIM+I+G 0.237 0.01 0.042194093 substitutions/site 0.0115 Chordata 15 0.144723103 0.991423539 0.434156352 0.014499364 5.177146416 "((bailloni:1.269,(viridis:0.509,(humboldti:0.128,inscriptus:0.157):0.190):0.70):0.5,(((aracari:0.425,(castanotis:0.292,pluricinctus:0.234):0.063):0.177,((beauhamaesil:0.326,biforquatus:0.346):0.271,(flavirostris:0.126,mariae:0.049):0.214):0.123):0.302,(torquaus:0.272,(frantzii:0.255,(erythropygius:0.062,sanguineus:0.024):0.102):0.117):0.763):0.165);" 026_Garcia_Moreno_etal_MPE "García-Moreno, J., N. Cortéz, G. M. García-Deras, and B. E. Hernández-Baños. 2006. Local origin and diversification among Lampornis hummingbirds: A Mesoamerican taxon. Mol. Phylo. Evol. 38:488-498." 100 3 "ND5, cytB & AK-5, c-mos" mtDNA & nuDNA 2943 Maximum Likelihood HKY+I+G 1.495 0.1 0.066889632 substitutions/site Chordata 10 0.944484463 1.550012477 . . . "((((((calolaema:0.12,cinereicauda:0.06):0.06,castaneoventris:0.143):0.562,(sybillae:0.743,viridipallens:0.804):0.076):0.452,((amathystinus:0.06,margaritae:0.060):0.266,salvini:0.14):0.828):0.036,clemenciae:1.306):0.554,hemileucus:2.623);" 027_Morse_Farrell_2005_MPE "Morse, G. E., and B. D. Farrell. 2005. Interspecific phylogeography of the Stator liombatus species complex: The geographic context of speciation and specialization. Mol. Phylo. Evol. 36:201-213." 100 3 COI mtDNA 665 Maximum Likelihood HKY85+I+G 0.265 0.000150376 0.000567456 substitutions/site 0.0115 Arthropoda 4 -1.260945343 0.077901668 2.998799712 4.496399858 0.204968808 "(((limbatusA:2.784,beali:2.065):0.59,limbatusB:2.553):1.086,limbatusC:4.438);" 028_Olsson_etal_MPE "Olsson, U., P. Alstrom, P. G. P. Ericson and P. Sundberg. 2005. Non-monophyletic taxa and cryptic species - Evidence from a molecular phylogeny of leaf-warblers (Phylloscopus, Aves). Mol. Phylo. Evol. 36:261-276." 100 3 "cyt b, 12S & myoglobin intron II" mtDNA & nuDNA 2172 Bayesian GTR+I+G 1.236 0.1 0.080906149 substitutions/site Chordata 38 -2.6917061 0.458024746 . . . "((((((((davisoni:0.155,halnanus:0.093):0.105,(xanthoschistos:0.285,davisoni:0.235):0.037):0.09,(((poliocephalus:0.246,amoenus:0.209):0.08,sarasinorum:0.23):0.01,trivirgatus:0.28):0.09,presbytes:0.23,trivirgatus:0.258):0.750,(reguloides:0.67,occipatalis:0.375):0.27):0.069,(ricketti:0.193,cantator:0.22):0.665):0.26,((((tenellipes:0.126,borealoides:0.27):0.35,magnirostris:0.529):0.126,borealis:0.69):0.259,((trochiloides:0.092,plumbeitarsus:0.168):0.085,nitidus:0.327):0.932,emeiensis:0.756):0.068):0.08,(((umbrovirens:0.777,ruficapilla:0.25):0.442,(whistleri:0.713,pollogenys:0.75):0.362):0.084,((coronatus:0.365,ijimae:0.648):0.234,cebuensis:0.622):0.46):0.12,castaniceps:1.242):0.414,((((trochilus:0.71,collybita:0.609):0.559,schwarzi:1.333,tytleri:1.187):0.25,orientalis:1.742):0.076,((proregulus:0.545,inornatus:1.143):0.114,maculipennis:0.888):0.328):0.288);" 029_Silva_Brandao_etal_MPE "Silva-Brandão, A. V. L. Freitas, A. V. Z. Brower, and V. N. Solferini. 2005. Phylogenetic relationships of the New World Triodini swallowtails (Lepidoptera: Papilionidae) based on COI, COII and EF-1a genes. Mol. Phylo. Evol. 36:468-483." 50 3 "COI., COII & EF-1a" mtDNA & nuDNA 3330 Bayesian GTR+I+G 1.305 0.1 0.076628352 substitutions/site Arthropoda 17 -1.214179796 0.652089388 . . . "((agavus:1.162,(proneus:1.97,(ascanius:0.255,unichus:0.651):1.424):0.101):0.097,((chabrias:1.419,(childrenae:0.82,(photinus:0.57,(sesosris:0.287,(vertumnus:0.244,anchises:0.287):0.111):0.288):0.304):0.393):0.189,((tros:0.586,aeneas:0.675):0.132,((lysander:0.272,panthonics:0.163):0.308,(neophilus:0.408,(eurimedes:0.182,zacynthus:0.147):0.062):0.241):0.231):0.579):0.197);" 030_Sota_etal_MPE "Sota, T., Y. Takami, G. B. Monteith, and B. P. Moore. 2005. Phylogenetic and character evolution of endemic Australian carabid beetles of the genus Pamborus based on mitochondrial and nuclear gene sequences. Mol. Phylo. Evol. 36:391-404." 85 5 "16S, ND5 & PepCK" mtDNA & nuDNA 2586 Maximum Likelihood GTR+I+G 4.4 50 11.36363636 Million years 1 Arthropoda 14 -0.676155327 0.592847068 0.069790496 0.000405893 28.36381391 "(((((((((sp_Cooloola:0.213,subtropicus:0.213):0.081,tropicus:0.294):0.079,transitus:0.373):0.145,opacus:0.5):0.362,((alternans:0.579,sp_Kroombit:0.579):0.09,viridis:0.68):0.189):0.111,elegans:0.98):0.241,(brisbanensis:0.824,macleayi:0.824):0.369):0.871,(pradieri:1.557,guerinii:1.54):0.516):0.431,punctatus:2.49);" 031_Takacs_etal_MPE "Takacs, Z., J. C. Morales, T. Geissmann, and D. J. Melnick. 2005. A complete species-level phylogeny of the Hylobatidae based on mitochondrial ND3-ND4 gene sequences. Mol. Phylo. Evol. 36:456-467." 100 4 "ND3, ND4" mtDNA 2243 Maximum Likelihood GTR+I+G 0.136 0.01 0.073529412 substitutions/site 0.0115 Chordata 12 -3.048399149 0.12110255 0.186934772 0.003494461 6.510200229 "(((((lar:0.56,((moloch:0.55,klossii:0.677):0.131,(agilis:0.458,muelleri:0.62):0.015):0.067):0.113,pileatus:0.506):0.369,syndactylus:1.011):0.103,(((gabriellae:0.439,leucogenys:0.347):0.182,concolor:0.279):0.089,sp_cf_nasutus:0.383):0.768):0.114,hoolock:0.76);" 032_Veyrunes_etal_MPE "Veyrunes, F., J. Britton-Davidian, T. J. Robinson, E. Calvet, C. Denys, and P. Chevret. 2005. Molecular phylogeny of the African pygmey mice, subgenus Nannomys (Rodentia, Murinae, Mus): Implications for chromosomal evolution. Mol. Phylo. Evol. 36:358-369." 100 3B cyt b & IRBP mtDNA & nuDNA 2362 Maximum Likelihood GTR+I+G 1.284 0.1 0.07788162 substitutions/site Chordata 12 -2.781089684 0.140961942 . . . "((platythrix:1.221,((cervicolor:0.831,(musculus:0.421,sprehes:0.484):0.5):0.3,(setulosus:0.88,((sp1:0.782,(mattheyi:0.475,minutoides:0.612):0.104):0.087,(minusoides:0.716,indutus:0.815):0.15):0.345):0.763):0.104):0.02,(pahari:0.56,crociduroides:0.68):0.79);" 033_Wilson_Lee_MPE "Wilson, N. G., and M. S. Y. Lee. 2005. Molecular phylogeny of Chromodoris (Mollusca, Nudibranchia) and the identification of a planar spawning clade. Mol. Phylo. Evol. 36:722-727." 100 2 16S mtDNA 416 Bayesian HKY+I+G 0.481 0.024038462 0.049976012 substitutions/site 0.0115 Mollusca 24 -1.963728919 0.369402227 0.241399961 0.002648816 9.621265038 "(((ambiguus:0.895,alternata:2.442):0.64,(luarna:0.51,(laevis:0.538,luteomarginata:0.427):0.316):1.001):0.49,((lochi:0.195,((quadricolor:0.447,strigata:0.366):0.1,(kuiteri:0.33,(magnifica:0.23,(aspersa:1.023,striatella:0.255):0.07):0.099):0.15):0.143):0.78,((luteorosea:0.535,(krohni:0.539,purpurea:0.672):0.449):0.61,((collingwoodi:0.409,kunlei:0.496):0.312,((roboi:0.229,(leopardus:0.462,geometrica:0.398):0.276):0.588,((splendida:0.625,daphne:0.507):0.153,(tasmaniensis:0.281,epicurea:0.281):0.465):0.315):0.181):0.166):0.512):0.445);" 034_Yokoyama_Goto_MPE "Yokoyama, R., and A. Goto. 2005. Evolutionary history of freshwater sculpins, genus Cottus (Teleostei: Cottidae) and related taxa as inferred from the mitochondrial DNA phylogey. Mol. Phylo. Evol. 36:654-668." 48 4 "12S, control region" mtDNA 1667 Maximum Likelihood HKY+I+G 0.295 0.01 0.033898305 substitutions/site 0.0115 Chordata 12 -3.444194507 0.068532846 0.367749017 0.013523934 3.047285672 "((aleuticus:0.477,((kesslerii:0.882,cognatus:0.519):0.144,gobio:0.34):0.119):0.138,(poecilopus:1.122,((reinii:0.487,pollux:0.777):0.35,czerskii:0.678):0.169):0.138,((amblystomaopsis:0.319,nozawae:0.552):0.506,(hangiongensis:0.535,koreanus:0.585):0.206):0.317);" 035_Ayoub_etal_MPE "Ayoub, N. A., S. E. Reichert, and R. L. Small. 2005. Speciation history of the North American funnel web spiders, Agelenopsis (Araneae: Agelenidae):Phylogenetic inferences at the population-species interface. Mol. Phylo. Evol. 36:42-57." 92 4 "COI, 16S" mtDNA 1081 Maximum Likelihood TrN+I+G 0.185 0.01 0.054054054 substitutions/site 0.0115 Arthropoda 13 -0.881155177 0.460956072 0.39597406 0.014254132 4.758317416 "(((((oklahoma:0.593,(((spatula:0.21,aleenae:0.183):0.251,sp_nov:0.371):0.09,aperta:0.617):0.109):0.042,longistylus:1.132):0.189,(((potteri:0.1,pensylvanica:0.059):0.03,emertoni:0.117):0.058,kastoni:0.062):0.221):0.058,naevia:0.335):0.558,(utahana:0.246,oregonensis:0.158):0.711);" 036_Barber&Bellwood_2005_MPE "Barber, P. H., and D. R. Bellwood. 2005. Biodiversity hotspots: evolutionary origins of biodiversity in wrasses (Halichoeres: Labridae) in the Indo-Pacific and new world tropics. Mol. Phylo. Evol. 35:235-253." 51 2 "COI, 16S, 12S" mtDNA 1810 Maximum Likelihood GTR+I+G 0.491 0.05 0.101832994 substitutions/site 0.0115 Chordata 56 -3.621053107 0.451257415 0.114554348 0.000243013 17.97297108 "(((((((T_lunare:0.351,(T_lutescens:0.382,(T_quinquevittatum:0.294,T_hardwicke:0.294):0.496):0.348):1.873,H_maculipinna:1.386):0.260,(((M_negrosensis:0.618,M_choati:0.507):0.052,M_meleagris:0.454):0.880,((((((H_prosopeion:0.296,(C_aurilineata:0.480,C_pictoides:0.451):0.152):0.109,H_solorensis:0.708):0.679,((H_marginatus:0.742,H_melanurus:0.410):0.117,(((H_binotopsis:0.654,H_papilionaceus:0.654):0.245,((H_argus:0.870,H_leucurus:0.700):0.094,H_nigrescens:1.153):0.055):0.110,H_richmondi:0.780):0.037):0.655):0.137,H_brownfieldi:1.215):0.253,(((H_melasmapomus:0.494,H_ornatissimus:0.411):0.151,H_chrysus:1.042):0.129,H_biocellatus:0.539):0.896):0.159,((C_batuensis:0.841,(H_podostigma:0.299,H_chloropterus:0.446):0.657):0.591,(H_miniatus:0.892,(H_margaritaceus:0.527,H_nebulosus:0.493):0.391):0.521):0.524):0.294):0.260):0.194,(((C_gaimard:0.568,(P_heteroptera:0.218,P_yamashiroi:0.410):0.444):0.690,((C_picta:0.677,(C_aygula:0.410,C_flavovittata:0.514):0.335):0.214,C_dorsomacula:1.287):0.198):0.147,(H_doliatus:0.0,H_annulatus:0.078):1.515):0.250):0.071,L_unilineata:1.662):0.052,((L_cyanopleura:2.028,H_hartzfeldii:1.454):0.591,((((H_dispilus:0.247,H_pictus:0.558):0.137,H_socialis:0.470):0.452,((H_nicholsi:0.201,(H_bivittatus:0.329,((H_radiatus:0.209,H_garnoti:0.264):0.039,H_poeyi:0.272):0.051):0.067):0.108,H_notospilus:0.300):0.306):0.381,H_semicinctus:0.864):0.482):0.069):0.09,(H_hortulanus:2.074,(H_scapularis:0.320,H_trimaculatus:0.411):0.795):0.386);" 037_Barker_etal_2004_MPE "Barker, N. P., A. Vanderpoorten, C. M. Morten, and J. P. Rourke. 2004. Phylogeny, biogeography, and the evolution of life-history traits in Leucadendron (Proteaceae). Mol. Phylo. Evol. 33:845-860." 65 2 ITS nuDNA ? Maximum Likelihood GTR+I+G 0.171 0.005 0.029239766 substitutions/site 0.00305 Magnoliophyta 60 -0.722698872 0.952978835 0.729655041 0.00917925 2.87758805 "((((ericifolium:0.158,((dregei:0.0,album:0.11):0.11,singulare:0.332):0.119):0.444,(((lanigerum:0.0,flexuosum:0.0,salignum:0.0,discolor:0.056):0.112,modestum:0.214):0.277,nervosum:0.41):0.056):0.085,(((((stellare:0.0,(levisanus:0.0,thymifolium:0.0):0.106):0.11,brunoiodes:0.0,galpinii:0.0):0.063,linifolium:0.211,verticillatum:0.211):0.272,(laxum:0.0,corymbosum:0.0):0.765):0.107,((((daphnoides:0.0,barkerae:0.0,(tinctum:0.0,elimense:0.0):0.07,burchelli:0.0):0.071,sessile:0.057,chamalaea:0.0):0.154,(loranthifolium:0.052,meyerianum:0.0,roodii:0.0,glaberrimum:0.0):0.055):0.226,((sericeum:0.0,nitidum:0.059):0.212,(pondoense:0.49,(floridum:0.0,(maxowanii:0.229,salicifolium:0.057):0.161):0.106,(laureolum:0.27,(loeriensis:0.264,xanthoconus:0.114):0.047,(spiddifoliuum:0.0,coniferum:0.0,conidum:0.0,meridianum:0.0,strobilium:0.0):0.06,gandogeri:0.0,microcephalum:0.0,(eucalypterfolium:0.169,uliginosum:0.113):0.065,spissifolium:0.0):0.109):0.274):0.066):0.063):0.062):0.082,osbornei:0.0,nobile:0.0,((argenteum:0.312,rubrum:0.05,(arcuatum:0.12,dubium:0.1):0.057):0.103,(((platyspermum:0.166,immoderatum:0.124,comosum:0.266):0.124,teretifolium:0.325):0.064,muirii:0.058):0.075):0.16);" 038_Burns_Naoki_2004_MPE "Burns, K. J., and K. Naoki. 2004. Molecular phylogenetics and biogeography of Neotropical tanagers in the genus Tangara. Mol. Phylo. Evol. 32:838-854." 88 2 "cyt b, ND2" mtDNA 1473 Bayesian GTR+I+G none Chordata 43 -3.699080026 0.380133452 . . . "((ruficervix:1.776,((cyanoptera:0.82,(viridicollis:0.224,(argyrofenges:0.063,heinei:0.095):0.177):0.931):0.602,((palmeri:2.69,(meyerdeschauenseei:0.526,(cayana:0.099,(vitriolina:0.296,cucullata:0.192):0.095):0.456):1.312):0.267,((nigrocincta:0.53,(larvata:0.642,cyanicollis:0.733):0.31):0.872,(varia:1.117,(guttata:1.321,(rufigula:1.308,(xanthogastra:0.884,punctata:1.574):0.22):0.134):0.308):0.854):0.17):0.193):0.283):0.706,((vassorii:1.396,((dowii:1.054,fucosa:1.47):0.376,nigroviridis:1.384):0.52):1.35,(labradondes:3.233,(cyanotis:2.351,(((inornata:0.893,mexicana:1.093):1.242,(chilensis:0.849,(callophrys:0.383,velia:0.48):0.352):1.111):0.226,((chrysotis:1.432,(xanthocephala:1.687,(parzudakii:1.54,(schrankii:0.966,(johannae:1.536,(arthus:1.457,(florida:0.87,icterocephala:0.781):0.316):0.546):0.26):0.244):0.243):0.373):0.432,(((desmaresti:0.647,cyanocephala:0.447):0.164,(seledon:0.522,fastuosa:0.402):0.603):0.804,(lavinia:1.058,gyrola:1.254):1.321):0.15):0.127):0.257):0.3):0.226):0.39);" 040_Cardenas_etal_MPE "Cárdenas, L., C. E. Hernández, E. Poulin, A. Magoulas, I. Kornfield, and F. P. Ojeda. 2005. Origin, diversificatino, and historical biogeography of the genus Trachurus (Perciformes: Carangidae). Mol. Phylo. Evol. 35:496-507." 79 5 cyt b mtDNA 1140 Maximum Likelihood TrN+I 0.957 0.005 0.00522466 substitutions/site 0.0115 Chordata 11 -0.920730218 0.451109096 0.649824553 0.046919106 2.231724877 "((((murphyi:0.809,symmetricus:0.809):1.454,picturatus:2.263):2.479,(trachurus:0.67,capensis:0.67):4.056):0.169,((lathami:1.224,trecae:1.224):2.958,(mediterraneus:3.944,(declivis:1.587,(japonicus:1.232,novaezelandiae:1.232):0.355):2.367):0.254):0.729);" 041_Carranza_Arnold_etal_2004_MPE "Carranza, S., E. N. Arnold, E. Wade, and S. Fahd. 2004. Phylogeography of the false smooth snakes, Macroprotodon (Serpentes, Colubridae): mitochondrial DNA sequences show European populations arrived recently from Northwest Africa. Mol. Phylo. Evol. 33:523-532." 100 2 "cyt b, 12S, 16S" mtDNA 1075 Maximum Likelihood GTR+I+G 0.21 0.01 0.047619048 substitutions/site 0.0115 Chordata 6 -0.963748115 0.327178947 0.334111541 0.02790763 2.926501059 "(abuakeri:0.516,((cucullatus:0.215,mauritanicus:0.215):0.67,((cucullatus:0.32,brevis_brevis:0.342):0.085,brevis_ibericus:0.14):0.44):0.096);" 042_Doadrio_Carmona_MPE "Doadrio, I., and J. A. Carmona. 2004. Phylogenetic relationships and biogeography of the genus Chondrostoma inferred from mitochondrial DNA sequences. Mol. Phylo. Evol. 33:802-815." 93 4 cyt b mtDNA 1140 Maximum Likelihood GTR+I+G 2.905 12 4.13080895 Million years 1 Chordata 25 -2.200934654 0.473512502 0.144658786 0.000909833 11.61451162 "(sp_e:2.81,soetta:2.81,(wilkommii:1.257,polylepis:1.257,duriense:1.257):1.553,genei:2.81,(sp_b:1.67,(arcasii:0.577,macrolepidotus:0.577):1.101):1.14,(regium:1.305,(oxyhinchum:1.08,((cyri:0.579,(prespense:0.375,vardarense:0.375):0.207):0.246,(nasus:0.709,(holmwoodii:0.551,meandrense:0.551):0.166):0.124):0.257):0.225):1.5,(toxostoma:0.782,(miegii:0.435,(arrigonis:0.378,turiense:0.378):0.068):0.35):2.025,(lusitanicum:1.668,(sp_d:1.513,(sp_c:0.983,lemmingii:0.983):0.542):0.177):1.139);" 044_Froufe_Weiss_MPE "Froufe, E., I. K. S. Weiss. 2005. Phylogenetic analysis of the genus Thymallus (grayling) based on mtDNA control region and ATPase 6 genes, with inferences on control region consraints and broade-scale Eurasian pylogeography. Mol. Phylo. Evol. 34:106-117." 100 3A "control region, ATPase 6" mtDNA 1768 Maximum Likelihood HKY+I+G 0.447 0.005 0.011185682 substitutions/site 0.0115 Chordata 10 -1.351856653 0.466317316 0.358570489 0.016071599 3.529062407 "(((grubii:1.219,orange_spot_form:1.305):2.487,lower_Amur_form:3.502):0.204,(large_scale_form:1.948,(((arcticus:0.525,nigrescens:0.216):0.437,(arcticus:0.952,brevirostris:1.382):0.323):0.616,arcticus:2.464):0.704):0.663,thymallus:4.009);" 045_Garrigues_etal_2005_MPE "Garrigues, T., C. Dauga, E. Ferquel, V. Choumet, and A.-B. Failloux. 2005.Molecular phylogeny of Vipera laurenti, 1768 and the related genera Macrovipera (Reuss, 1927) and Daboia (Gray, 1842), with comments about neurotoxic Vipera aspis aspis populations. Mol. Phylo. Evol. 35:35-47." 71 4 "cyt b, ND2" mtDNA 1708 Maximum Likelihood GTR+I+G 0.232 0.01 0.043103448 substitutions/site 0.0115 Chordata 6 -0.985953649 0.293866497 0.079104589 0.001564384 12.70450704 "(ammodytes:3.733,((ursinii:1.713,(seoanei:1.245,berus:0.612):0.101):1.012,(latastei:2.127,aspis:1.343):1.236):0.369);" 047_Goropashnaya_etal_2004_MPE "Goropashnaya, A. V., V. B. Fedorov, and P. Pamilo. 2004. Recent speciation in the Formica rufa group ants (Hymenoptera, Formicidae): inference from mitochondrial DNA phylogeny. Mol. Phylo. Evol. 32:198-206." 100 2 "cyt b, ND1" mtDNA 2051 Neighbor Joining 0.859 0.002 0.002328289 substitutions/site 0.0115 Arthropoda 6 1.014421672 2.469230092 2.170144719 1.177382025 0.579440271 "(((lugubris:0.234,pratensis:0.234,aquilonia:0.234):2.586,pratensis:2.56):0.996,(polyctena:0.222,rufa:0.222):1.816);" 048_Hillis_Wilcox_2005_MPE "Hillis, D. M., and T. P. Wilcox. 2005. Phylogeny of the New World frogs (Rana). Mol. Phylo. Evol. 34:299-314." 88 1 "12S, 16S" mtDNA 2000 Maximum Likelihood GTR+I+G 0.166 0.01 0.060240964 substitutions/site 0.0115 Chordata 57 -2.795377876 0.494312969 0.270270389 0.001328111 9.01652127 "((temporaria:1.122,((boylii:0.777,luteiventris:0.388):0.108,(muscosa:0.312,(aurora:0.202,cascadae:0.229):0.195):0.263):0.118):0.55,((sylvatica:0.805,((septentrionalis:0.426,(grylio:0.767,((okaloosae:0.07,clamitans:0.077):0.136,(heckscheri:0.38,catesbaeiana:0.328):0.043):0.085):0.047):0.1,vigratipes:0.557):0.565):0.198,(((maculata:0.95,(vibicaria:0.712,warszewitschii:1.254):0.937):0.221,(((palmipes:1.485,sp_1:0.21):0.122,bwana:0.365):0.207,(vaillanti:0.952,juliani:0.78):0.191):0.894):0.269,((sierramadrensis:1.43,((psilonota:1.018,zweifeli:0.719):0.219,(tarahumarae:0.421,pustulosa:1.081):0.183):0.53):0.37,((pipiens:0.407,((dunni:0.132,montezumae:0.225):0.211,(sp_2:0.251,(chiracahuensis:0.288,sumaquavocalis:0.098):0.123):0.071):0.277):0.443,((palustris:0.303,(areolata:0.463,(sevosa:0.025,capito:0.115):0.286):0.115):0.197,(((spectabilis:0.558,(orniltemana:0.707,sp_3:0.391):0.05):0.032,((((flaloci:0.03,neovolcanica:0.0):0.05,berlandieri:0.072):0.088,blairi:0.085):0.306,(sphenocephala:0.205,utricularia:0.127):0.222):0.065):0.079,(forreri:0.68,(((magnaocularis:1.046,sp_7:0.715):0.227,((yavapaiensis:0.09,onca:0.09):0.301,sp_8:0.893):0.069):0.071,((macroglossa:0.316,taylori:0.676):0.166,((sp_4:0.221,sp_5:0.383):0.06,sp_6:0.4):0.073):0.092):0.033):0.066):0.369):0.087):1.104):0.11):0.4):0.131);" 049_Hundsdoerfer_etal_2005_MPE "Hundsdoerfer, A. K., I. J. Kitching, and M. Wink. 2005. A molecular phylogeny of the hawkmoth genus Hyles (Lepidoptera: Sphingidae, Macroglossinae). Mol. Phylo. Evol. 35:442-458." 59 4B "COI, COI" mtDNA 2300 Maximum Likelihood GTR+I+G 1.56 0.1 0.064102564 substitutions/site 0.0115 Arthropoda 19 -0.700603602 0.663676208 0.446708343 0.011738138 5.081837454 "(lineata:0.912,((euphorbiarum:0.398,annei:0.392):0.248,(livornicoides:0.388,(calida:0.933,((nicaea:0.149,gallii:0.241):0.147,(livornica:0.393,(vespertilio:0.324,((dahlii:0.135,(siehei:0.308,(hippophaes:0.243,sammuti1:0.317):0.044):0.016):0.050,((costata:0.149,tithymali:0.035,sammuti2:0.093):0.086,(euphorbiae:0.055,robertsi:0.039,sammuti3:0.034):0.057):0.070):0.111):0.054):0.108):0.140):0.092):0.092):0.237);" 052_Ketmaier_etal_2004_MPE "Ketmaier, V., P. G. Bianco, M. Cobolli, M. Krivokapic, R. Caniglia, and E. De Matthaeis. 2004. Molecular phylogeny of two lineages of Leuciscinae cyprinids (Telestes and Scardinius) from the peri-Mediterranean area based on cytochrome b data. Mol. Phylo. Evol. 32:1061-1071." 80 2 cyt b mtDNA 1140 Maximum Likelihood GTR+G 0.144 0.01 0.069444444 substitutions/site 0.0115 Chordata 14 -2.010232453 0.368488139 0.161353727 0.002169585 9.877423783 "(((S_acamaeicus:0.063,S_graecus:0.124):0.169,(S_erythrophthalmus:0.624,S_scardafa:0.452):0.26):0.831,((T_souffia:0.826,((T_mulitcellus:1.249,T_montenigrinus:0.687,(L_turskyi:0.558,L_polylepis:0.501):0.072):0.134,(T_pleurobipunctatus:0.911,T_beoticus:0.594):0.198,(P_croaticus:0.337,P_metohiensis:0.496):0.508):0.145):0.726,L_cephalus:1.677):0.228);" 053_Kizirian_etal_2004_MPE "Kizirian, D., A. Trager, M. A. Donnelly, and J. W. Wright. 2004. Evolution of Galapagos Island Lava Lizards (Iguania: Tropiduridae: Microlophus). Mol. Phylo. Evol. 32:761-769." 88 2 "ND1, ND2, COI" mtDNA 1956 Maximum Likelihood GTR+I+G 0.39 0.05 0.128205128 substitutions/site 0.0115 Chordata 9 -0.599281127 0.813557684 0.075627823 0.000817081 16.85165828 "(((dundanensis:0.367,(pacificus:0.23,grayii:0.335):0.031):0.326,delanonis:0.559):0.562,((((habelii:0.173,bivitattus:0.0):0.762,occipitalis:1.020):1.023,stolzmanni:1.401):0.18,koepckeorum:1.538):0.15);" 054_Klanten_etal_2004_MPE "Klanten, S. O., L. van Herwerden, J. H. Choat, and D. Blair. 2004. Patterns of lineage diversification in the genus Naso (Acanthuridae). Mol. Phylo. Evol. 32:221-235." 100 2 "16S, cyt b & ETS2" mtDNA & nuDNA 1332 Maximum Likelihood HKY+G 0.374 0.007507508 0.020073549 substitutions/site Chordata 20 -1.521815196 0.386779792 . . . "((((((annulatus:0.333,brachycentron:0.303):0.087,(fageni:0.506,mcdadei:0.465):0.142):0.179,(tonganus:0.082,tuberosus:0.184):0.285):0.159,lopezi:0.548):0.567,(((brevirostris:0.51,(((caesius:0.056,sp_1:0.126):0.106,hexacanthus:0.049):0.785,vlamingii:0.231):0.171):0.334,((elegans:0.241,lituratus:0.0):0.345,unicornis:0.654):0.531):0.142,(maculatus:0.287,reticulatus:1.059):0.538):0.464):0.393,((caeruleacauda:0.733,thynnoides:0.601):0.243,minor:0.903):0.292);" 055_Lijtmaer_etal_2004_MPE "Lijtmaer, D. A., N. M. M. Sharpe, P. L. Tubaro, and S. C. Lougheed. 2004. Molecular phylogenetics and diversification of the genus Sporophila (Aves: Passeriformes). Mol. Phylo. Evol. 33:562-579." 68 4 cyt b mtDNA 303 Maximum Likelihood HKY+G 0.158 0.00330033 0.020888165 substitutions/site 0.0115 Chordata 28 0.157378868 0.97520531 0.962561891 0.035635592 2.413567971 "(((((((O_angolensis:0.818,(collaris:0.334,leucoptera:0.162):0.658):0.321,(((collaris:0.0,nigricollis:0.168):0.166,caerulescens:0.0):0.324,luctuosa:0.962,nigricollis:0.487):0.648):0.325,americana:1.632):0.15,(falcirostris:0.655,schistracea:0.173):0.467):0.326,(((bouvreuil:0.243,zelichi:0):0.187,bouvreuil:0.187,((minuta:0.163,castaneiventris:0.327,minuta:0.343):0.496,melanogaster:0.0):0.332,cinnamomea:0.0,hypochroma:0.0,hypoxantha:0.0,palustris:0.0,ruficollis:0.183,zelichi:0.0):0.174,palustris:0.0):0.959):0.349,O_crassirostris:0.821):0.336,(telasco:0.792,castaneiventris:0.982):0.159);" 056_Luo_etal_2004_MPE "Luo, J., D. Yang, H. Suzuki, Y. Wang, W.-J. Chen, K. L. Campbell, and Y.-P. Zhang, 2004. Molecular phylogeny and biogeography of Oriental voles: genus Eothenomys (Muridae, Mammalia). Mol. Phylo. Evol. 33:349-362." 89 3 cyt b mtDNA 1143 Maximum Likelihood GTR+I+G 0.422 0.05 0.118483412 substitutions/site 0.0115 Chordata 15 -1.019379628 0.453162334 0.145731528 0.001633668 12.56857868 "(((((cachunus:0.253,fidelis:0.154):0.034,(eleusis:0.039,miletus:0.037):0.13):0.175,melanogaster:0.691):0.277,(custos:1.213,(olitor:0.448,proditor:0.51):0.299):0.203):0.235,(((smithii:0.159,andersoni:0.159):0.256,(rex:0.395,rufocanus:0.346):0.032):0.471,(glareolus:0.418,(rutilus:0.553,gapperi:0.407):0.066):0.36):0.339);" 057_Malhotra&Thorpe_2004_MPE "Malhotra, A., and R. S. Thorpe. 2004. A phylogeny of four mitochondrial gene regions suggests a revised taxonomy for Asian pitvipers (Trimeresurus and Oviphis). Mol. Phylo. Evol. 32:83-100." 82 1 "12S, 16S, ND4" mtDNA 2403 Bayesian GTR+I+G 0.746 0.1 0.134048257 substitutions/site 0.0115 Chordata 27 -2.442332307 0.358474183 0.075801286 0.000229833 26.63687 "((((((albolabris:0.742,(((erythrurus:0.155,pupureomaculatus:0.181):0.231,cantori:0.329):0.055,andersoni:0.317):0.150):0.140,septentrionalis:0.704):0.164,insularis:0.629):1.342,((venustus:0.502,macrops:0.260):0.204,kanburiensis:0.523):1.144,(((gumprechti:0.468,stejnegeri:0.625):0.227,vogeli:0.792):0.235,medoensis:0.758):0.142):0.355,((((flavomaculatus:0.257,mcgregori:0.206):0.638,(sumatranus:0.868,schultzei:0.690):0.176):0.156,malcomi:0.587):0.316,hageni:1.066):0.479,(popeiorum:1.560,tibetanus:0.991):0.193):0.371,(((gramineus:0.681,trigonocephalus:0.630):0.457,malabaricus:1.480):0.809,(puniceus:1.655,borneensis:1.924):0.472):0.343);" 058_Mallarino_etal_2005_MPE "Mallarino, R., E. Bermingham, K. R. Willmott, A. Whinnett, and C. D. Jiggins. 2005. Molecular systematics of the butterfly genus Ithomia (Lepidoptera: Ithomiinae): a composite phylogenetic hypothesis based on seven genes. Mol. Phylo. Evol. 34:625-644." 96 7 "COI, COII & EF-1a, tektin, wingless, ribosomal L5." mtDNA & nuDNA 4469 Bayesian GTR+I+G 0.363 0.005 0.013774105 substitutions/site Arthropoda 23 -2.880236179 0.258892884 . . . "(((((agnosia:1.124,(pseudoagalla:1.154,dalmeidai:0.758):0.068):0.065,drymo:0.953):0.586,((amarilla:0.838,arduinna:0.922):0.318,jucunda:1.187):0.630):0.469,terra:2.343):0.830,(((avella:1.187,(((eleonara:0.406,ellara:0.135):0.214,praeithomia:0.551):0.602,hymettia:1.023):0.106):0.258,(((celemia:1.308,herladica:0.760):0.276,(((cleora:0.997,(iphianassa:0.084,salapia:0.175):0.327):0.285,diasia:0.410):0.5,patilla:0.801):0.377):0.088,hyala:1.396):0.393):0.359,(lagusa:1.248,xenos:0.980):0.486):0.802);" 059_Minegishi_etal_2005_MPE "Minegishi, Y., J. Aoyama, J. G. Inoue, M. Miya, M. Nishida, and K. Tsukamoto. 2005. Molecular phylogeny and evolution of the freshwater eels genus Anguilla based on the whole mitochondrial genome sequences. Mol. Phylo. Evol. 34: 134-146." 100 3 total mt genome mtDNA 15187 Bayesian GTR+I+G 2.679 0.1 0.037327361 substitutions/site 0.0115 Chordata 15 -3.474078003 0.140294713 0.247243488 0.004702257 5.330135409 "(mossambica:1.384,((borneonsis:1.687,((anguilla:0.46,rostrata:0.418):0.88,(dieffenbachii:0.75,australis:1.152):0.153):0.1):0.125,(japonica:1.074,(reinhardtii:1.073,((celebesensis:0.823,megastoma:0.848):0.29,(marmorata:0.641,(mebulosa:0.724,(interioris:0.59,(obscura:0.56,bicolor:0.863):0.183):0.057):0.109):0.415):0.078):0.063):0.399):0.317);" 060_Moussalli_etal_2005_MPE "Moussalli, A., A. F. Hugall, and C. Moritz. 2005. A mitochondrial phylogeny of the rainforest skink genus Saproscincus, Wells and Wellington (1984). Mol. Phylo. Evol. 34:190-202." 100 2 "ND4, 16S" mtDNA 1743 Bayesian GTR+I+G 0.964 0.1 0.10373444 substitutions/site 0.0115 Chordata 11 -2.593923553 0.212902338 0.062335374 0.000431744 19.59594311 "(((lewisi:1.505,basciliscus:1.693):0.277,(tetradactyla:1.253,(cxechrual:1.269,hannahae:1.481):0.333):0.472):0.444,(((sp_1:0.955,(rosei:1.107,spectabilis:0.906):0.401):0.25,chalenegeri:1.077):0.46,(mustelinus:0.248,oriarus:0.068):1.513):0.294);" 061_Near_etal_2004_MPE "Near, T. J., D. I. Bolnick, and P. C. Wainwright. 2004. Investigating phylogenetic relationsihps of sunfishes and black basses (Actinopterygii: Centrarchidae) using DNA sequences from mitochondrial and nuclear genes. Mol. Phylo. Evol. 32:344-357." 100 3 "ND2 & S7 ribosomal, Tmo-4C4" mtDNA & nuDNA 2272 Bayesian GTR+I+G 0.22 0.01 0.045454545 substitutions/site Chordata 32 -2.637517673 0.404587684 . . . "((C_macropterus:0.785,(E_chaetodon:0.533,(E_gloriousus:0.213,E_obesus:0.203):0.378):0.436,((A_interruptus:0.614,((A_ariommus:0.182,A_rupestris:0.334):0.347,(A_cavifrons:0.326,A_constellatus:0.420):0.092):0.341):0.197,(P_annularis:0.705,P_nigromaculatus:0.744):0.369):0.122):0.173,(A_pomotis:1.343,(((M_dolomieu:0.141,M_punctulatus:0.106):0.452,(M_coosae:0.405,(M_cataractae:0.330,M_notius:0.370):0.065,(M_treculi:0.371,(M_salmoides:0.170,M_floridanus:0.290):0.116):0.100):0.096):0.867,((L_gulosus:0.606,(L_symmetricus:0.356,L_cyanellus:0.188):0.371):0.557,((L_humilis:0.420,L_macrochirus:0.442):0.478,((L_auritus:0.412,(L_marginatus:0.357,L_megalotis:0.288):0.184):0.638,(L_gibbosus:0.587,(L_microlophus:0.295,(L_punctatus:0.260,L_miniatus:0.325):0.177):0.521):0.179):0.430):0.145):0.764):0.305):0.117);" 062_Neves_etal_2005_MPE "Neves, S. S., G. Swire-Clark, K. W. Hilu, and W. B. Baird. 2005. Phylogeny of Eleusine (Poaceae: Chloridoideae) based on nuclear ITS and plastid trnT-trnF sequences. Mol. Phylo. Evol. 35:395-419." 80 6 "ITS, trnT-trnF" nuDNA 4859 Bayesian GTR+I+G 0.434 0.01 0.023041475 substitutions/site Magnoliophyta 9 -1.650775064 0.288755922 . . . "(((((((coracana:0.292,indica:0.072):0.062,kigeziensis2:0.169):0.051,kigeziensis1:0.225):0.060,tristachya:0.207):0.337,(floccifolia:0.292,intermedia:0.297):0.271):0.210,multiflora:0.718):0.106,jaegeri:0.372);" 063_Overton_Rhodes_2004_MPE "Overton, L. C., and D. D. Rhoads. 2004. Molecular phylogenetic relationships based on mitochondrial and nuclear gene sequences for the Todies (Todus, Todidae) of the Caribbean. Mol. Phylo. Evol. 32:524-538." 100 6B "cyt b, ATPase 6, ATPase 8 & c-mos" mtDNA & nuDNA 2511 Maximum Likelihood HKY+G 1.732 0.1 0.057736721 substitutions/site Chordata 5 -2.233634805 6.25E-04 . . . "(((todus:1.041,mexicanus:1.538):0.632,sublatus:0.649):0.497,(multicolor:1.281,angustirostris:1.409):0.393);" 064_Stenson_etal_2004_MPE "Stenson, A. G., R. S. Thorpe, and A. Malhotra. 2004. Evolutionary differentiation of maculatus group anoles based on analyses of mtDNA and microsatellite data. Mol. Phylo. Evol. 32:1-10." 100 1A "cyt b, COI" mtDNA 1005 Maximum Likelihood GTR+G 0.379 0.1 0.263852243 substitutions/site 0.0115 Chordata 10 -2.866495404 0.104379131 0.10159003 0.001290067 10.64066624 "((((marmoratus:0.345,oculatus:0.311):0.044,(lividus:0.268,(ferreus:0.313,(nubilus:0.249,(marmoratus:0.213,sabanus:0.1):0.05):0.064):0.13):0.084):0.165,leachii:0.377):0.095,(bimaculatus:0.3,gingivinus:0.246):0.087);" 065_Swigonova&Kjer_2004_MPE "Swigo?ová, Z., and K. M. Kjer. 2004. Phylogeny and host-plant association in the leaf beetle genus Trirhabda LeConte (Coleoptera: Chrysomelidae). Mol. Phylo. Evol. 32:358-374." 100 2 "COI, 12S & ITS2" mtDNA & nuDNA 1500 Bayesian GTR+G 0.26 0.1 0.384615385 substitutions/site Arthropoda 21 -2.476795589 0.390345237 . . . "(pubicollis:0.506,((adela:0.536,(schwarzi:0.288,geminata:0.191):0.367):0.273,(((bacharidis:0.373,(nigrivenris:0.155,canadensis:0.138):0.053):0.143,(virgata:0.111,(borealis:0.088,convergens:0.053):0.047):0.051):0.184,((pilosa:0.201,lewisii:0.303):0.149,((diducta:0.067,eriodictyonis:0.211):0.239,((flavolimbata:0.234,manisi:0.119):0.092,(sericotraschyla:0.356,(nitidicolus:0.185,(luteocincta:0.327,(confusa:0.178,lufeocincta:0.160):0.053):0.082):0.052):0.056):0.209):0.066):0.072):0.108):0.073);" 067_Xiao_etal_2005_MPE "Xiao, H., S.-y. Chen, X.-m. Liu, R.-d. Zhang, W.-x. Li, R.-g. Zan, and Y.-p. Zhang. 2005. Molecular phylogeny of Sinocyclocheilus (Cypriniformes: Cyprinidae) inferred from mitochondrial DNA sequences. Mol. Phylo. Evol. 36:67-77." 100 4 "ND4, cyt b" mtDNA 2172 Bayesian GTR+I+G 1.369 0.1 0.073046019 substitutions/site 0.0115 Chordata 31 0.531037263 1.73721693 0.250925576 0.00217116 11.06688593 "((((((((((((macrocephalus:0.137,(huaningensis:0.112,guishanensis:0.192):0.05):0.032,(oxycephalus:0.0,lunanensis:0.0):0.206):0.094,malacopterus:0.183):0.076,angustiporus:0.267):0.175,yangzongensis:1.057):0.056,((grahami:0.216,tingi:0.293):0.353,(maitianheensis:0.037,anophthalmus:0.034):0.634):0.435):0.106,(lateristritus:0.077,qujingensis:0.307):0.442):0.523,((multipunctatus:0.082,cyphotergous:0.097):1.237,macrolepis:1.651):0.064):0.059,((lingyunensis:0.090,longibarbatus:0.070):0.143,macrophthalmus:0.233):0.827):0.168,((microphthalmus:0.090,halfibindus:0.085):1.086,anatirostris:0.763):0.457):0.099,((((furcodorsalis:0.123,jiuxuensis:0.080):0.040,bicornutus:0.305):0.092,(tianeensis:0.212,altishoulderus:0.050):0.161):0.352,(rhinocerous:0.539,hyalinus:0.611):0.158):0.51):0.623,jii:1.49);" 068_Yi_etal_2004_MPE "Yi, T., A. J. Miller, and J. Wen. 2004. Phylogenetic and biogeographic diversification of Rhus (Anacardiaceae) in the Northern Hemisphere. Mol. Phylo. Evol. 33:861-879." 100 6 "ITS & ndhF, trnL-F" chlDNA & nuDNA 3866 Maximum Likelihood GTR+I+G 0.1 1 10 Million years 1 Magnoliophyta 16 -1.021201062 0.544164585 0.062983624 0.000283353 27.825 "((((sandwicensis:0.978,chinensis:0.978):1.064,(punjabensis:1.755,coriaria:1.755):0.310):0.404,((capallina:0.267,lanceolata:0.267):2.106,(typhina:0.454,glabra:0.454):1.924):0.087):0.338,(((ovata:0.252,integrifolia:0.252):1.274,((virens:0.516,choriophylla:0.516):0.484,(schiedeana:0.55,kearneyi:0.55):0.434):0.542):0.523,(trilobata:0.451,aromatica:0.451):1.554):0.738);" 069_Yu_etal_MPE "Yu, L., Q.-w. Li, O. A. Ryder, and Y.-p. Zhang. 2004. Phylogeny of the bears (Ursidae) based on nuclear and mitochondrial genes. Mol. Phylo. Evol. 32:480-494." 100 4 "IRBP, TTR" nuDNA 2293 Maximum Likelihood TrN+I 0.185 0.01 0.054054054 substitutions/site Chordata 7 -0.118171736 0.799919098 . . . "((((U_arctos:0.37,U_maritimus:0.215):0.215,(U_thibetanus:0.469,U_americanus:0.133):0.136):0.486,(H_malayanus:0.234,M_ursinus:0.529):0.516):0.483,T_ornatus:1.548);" 070_Bell_etal_2004_MPE "Bell, K. L., D. K. Yeates, C. Moritz, and G. B. Montgeith. 2004. Molecular phylogeny and biogeography of the dung beetle genus Temnoplectron Westwood (Scarabaeidae: Scarabaeinae) from Australia's wet tropics. Mol. Phylo. Evol. 31:741-753." 79 2 COII mtDNA 1330 Maximum Likelihood GTR+G 8.3 0.05 0.006024096 substitutions/site 0.0115 Arthropoda 15 -4.344309063 0.077086285 0.079159906 0.000482022 13.89225291 "(((T_rotundum:19.4,T_boucomonti:18.5):3.2,T_major:19.5):3.1,((((T_aeneopiceum:19.1,T_subvolitans:14.4):5.5,(T_involucre:23.2,(T_lewisense:13.9,T_monteithi:18.0):3.0):4.9):3.2,((((T_reyi:12.4,T_politulum:1.4):9.5,T_cooki:18.0):4.7,T_finnigani:22.3):3.1,T_disruptum:21.7):2.2):5.4,(T_laeve:26.1,T_bornemisszai:14.2):5.4):0.4);" 071_Banford_etal_2004_MPE "Banford, H. M., E. Bermingham, and B. B. Collette. 2004. Molecular phylogenetics and biogeography of transisthmian and amphi-Atlantic needlefishes (Belonidae: Strongylura and Tylosurus): perspectives and New World marine speciation. Mol. Phylo. Evol. 31:833-851." 100 5 "ATPase8, ATPase6, cyt b, 12S, 16S & CK" mtDNA & nuDNA 3689 Maximum Likelihood GTR+I+G 1 1 1 substitutions/site Chordata 9 -1.717124856 0.305516877 . . . "((((((marina:0.059,sp:0.045):0.006,exilis:0.041):0.019,hubbsi:0.061):0.026,(scapularis:0.106,fluviatilis:0.053):0.024):0.058,(timucu:0.016,senegalensis:0.016):0.071):0.016,notata:0.097);" 072_Artiss_etal_2001_MPE "Artiss, T., T. R. Schultz, D. A. Polhemus, and C. Simon. 2001. Molecular phylogenetic analysis of the dragonfly genus Libellula, Ladona, and Plathemis (Odonata: Libellulidae) based on mitochondrial cytochrome oxidase I and 15S rRNA sequence data. Mol. Phylo. Evol. 18:348-361." 84 2 "COI, 16S" mtDNA 1151 Maximum Likelihood GTR+I+G 9 0.012019231 0.00133547 substitutions/site 0.0115 Arthropoda 27 0.804371834 1.161796282 0.761321979 0.023184446 4.022779958 "((L_lydia:0,L_subornata:2.2):18.4,(O_ferruginea:25.1,(L_fulva:18.1,(L_depressa:9.1,(L_exusta:15.1,(L_deplenata:14.9,L_julia:15.15):7.1):13.4):8.1):23.0,(L_flavida:0,(L_needhami:2.7,(L_vibrans:3.9,(L_axilena:0,(L_comanche:3.9,(L_cyanea:0,(L_luctuosa:4.6,(L_auripennis:2.6,L_incesta:2.6,L_jesseana:2.5):2.3):1.1):2.1,((L_pulchella:6.0,(L_forensis:2.7,L_nodistica:0):1.7):3.8,((L_angelina:9.3,(L_quadrimaculata:9.8,L_semifasciata:27.3):3.5):7.3,(L_composita:6.0,(L_croceipennis:20.2,L_saturata:14.4):2.1):5.2):2.3):3.4):2.2):1.1):1.8):4.2):18.7):18.2);" 073_Austin_etal_2004_MPE "Austin, J. J., E. N. Arnold, and C. G. Jones. 2004. Reconstructing an island radiation using ancient and recent DNA: the extinct and living day geckos (Phelsuma) of the Mascarene islands. Mol. Phylo. Evol. 31:109-122." 58 2 "12S, cyt b & c-mos" mtDNA & nuDNA 1460 Maximum Likelihood GTR+I+G 11.2 0.05 0.004464286 substitutions/site Chordata 16 -3.563096824 0.133933047 . . . "(((((((cepediana:12.9,guentheri2:15.4):4.0,borbonica:10.6):4.5,(ornata:12.7,guimbeaui:12.4):4.2):9.1,guentheri:17.0):8.0,((abbotti:20.9,mutabilis2:20.2):13.3,astriata:19.9):8.8):1.1,((((lineata:19.1,laticauda:24.0):2.9,quadriocellata:21.5):5.1,serraticauda:38.3):11.9,mutabilis:33.5):3.0):2.9,(andamanensis:44.2,standingi:22.6):3.2);" 074_Austin_1996_MPE "Austin, J. J. 1996. Molelucar phylogenetics of Pufinus shearwaters: Preliminary evidence from mitochondrial cytochrome b gene sequences. Mol. Phylo. Evol. 6:77-88." 53 4a cyt b mtDNA 575 Maximum Likelihood 9.3 0.01 0.001075269 substitutions/site 0.0115 Chordata 17 -0.664002924 0.570431506 0.421145823 0.011824254 5.824243887 "(((((puffinis:17.4,newelli:12.1,(therminieri:6.2,(baroli:0.0,boydi:0.0):2.9):5.9):2.8,assimilis:14.5,(huttoni:28.8,gavia:9.7):17.1):11.4,pufinus:19.9):16.1,nativitatis:47.3):31.3,(((pacificus:18.6,bulleri:14.7):14.3,(tenulrostris:19.6,(griseus:19.8,gravis:7.0):3.3):3.2):3.3,(carneipes:3.8,creatopus:3.8):4.1):29.5);" 075_Becerra_2003_MPE "Becerra, J. X. 2003. Evolution of Mexican Bursera (Burseraceae) inferred from ITS, ETS, and 5S nuclear ribosomal DNA sequences. Mol. Phylo. Evol. 26:300-309." 73 3 "ITS, 5S-NTS, ETS" nuDNA doesn't say Maximum Likelihood HKY85+G 7 0.01 0.001428571 substitutions/site 0.00305 Magnoliophyta 64 -4.808304955 0.296887129 0.135333365 0.000295405 24.94203914 "((((((filicifolia:8.2,(bicolor:8.1,sarukhanii:7.5):1.0):1.2,(palmeri:8.45,((bipinnata:9.7,stenophylla:6.6):2.4,hindsiana:6.5):1.3):1.8):0.9,((((((asplenifolia:8.2,hintonii:3.4):2.0,copallifera:2.8):1.5,velutina:10.4):2.7,diversifolia:18.8):1.7,excelsa:7.9):1.3,(submoniliformis:5.3,vejar_vazquezii:6.9):3.3):0.9):3.1,(((((bonetti:6.3,mirandae:4.8):0.3,biflora:15.7):4.9,(((penicillata:7.9,citronella:3.5):3.0,infiernidialis:10.7):2.9,((xochipalensis:12.0,glabrifolia:13.9):4.5,(aloexylon:6.1,heteresthes:8.6,coyucensis:8.4):3.1):2.9):0.9):0.5,epinnata:54.5):2.0,((ruticola:4.8,cerasifolia:6.7):2.2,sarcopoda:36.9):9.2):2.1):15.7,tecomaca:31.7):14.0,((((((((paradoxa:21.2,ariensis:15.6):5.2,fagaroides2:33.3):7.4,discolor:13.3):2.6,((((bolivarii:4.5,(schlechtendalii:0,medranoana:13.2):6.0):1.9,chemapodicta:10.8):2.0,fagaroides:29.3):4.9,(trifoliolata:12.8,aptera:3.3):3.3):5.2):3.1,odorata:16.0):8.0,(((((crenata:32.0,kerberii:9.7):13.8,denticulata:31.5):1.2,(lancifolia:18.1,trimera:2.4):2.8):8.2,fragilis:7.3):6.7,multijuga:6.7):2.1):0.5,(((((suntui:10.1,galeottiana:23.4):1.5,morelensis:7.3):4.3,arida:4.5):4.3,rzedowski:21.3):6.5,microphylla:13.8):3.1):9.9,(((((cinerea:4.4,longipes:1.6):2.3,(acuminata:20.1,atenuata:7.4):1.8):2.8,(instabilis:8.8,arborea:9.9):2.1):0.9,grandifolia:19.6):3.1,simaruba:18.5):10.3):24.5);" 076_Blum_etal_2003_MPE "Blum, M. J., E. Bermingham and K. Dasmahapatra. 2003. A molecular phylogeny of the neotropical butterfly genus Anartia (Lepidoptera: Nymphalidae). Mol. Phylo. Evol. 26:46-55." 100 2 "COI, COII & Tpi" mtDNA & nuDNA 2247 Maximum Likelihood GTR+G none Arthropoda 5 -0.706442577 0.122109533 . . . "((jatrophae:32.9,(fatima:15.0,amathea:14.4):18.5):19.5,(lytrea:25.9,chrysopelea:25.6):26.7);" 077_Alfaro&Arnold_2001_MPE "Alfaro, M. E., and S. J. Arnold. 2001. Molecular systematics and evolution of Regina and the Thamnophiine snakes. Mol. Phylo. Evol. 21:408-423." 64 3 "cyt b, 12S, ND2" mtDNA 3039 Maximum Likelihood GTR+I+G 3.5 0.05 0.014285714 substitutions/site 0.0115 Chordata 26 -3.732598896 0.275452972 0.041063791 7.02598E-05 37.28600469 "((((C_kirtlandi:22.7,V_striatula:31.1):2.0,(S_occipitomaculata:19.9,S_dekayi:24.5):5.7):1.0,(R_alleni:31.5,(R_rigida:17.4,S_pygaea:15.8):2.5):2.8):5.4,(((N_cyclopion:8.1,N_floridana:9.5):14.5,(((((N_fasciata:12.1,N_sipedon:11.5):3.7,N_eryhrogaster:13.9):0.8,(N_taxispilota:8.4,N_rhombifer:11.4):7.0):4.4,(R_grahami:21.8,T_lineatum:21.7):2.5):1.0,R_septemvittata:20.4):0.3):2.0,((((((T_butleri:0.8,T_radix:0.9):3.5,T_elegans:5.5):3.6,(T_ordinoides:5.3,T_atratus:6.6):1.2):3.4,T_marcianus:13.4):5.0,T_cyrtopsis:14.3):6.4,(T_proximus:20.9,T_sirtalis:15.1):3.0):4.2):0.6);" 078_Collins&Dubach_2001_MPE "Collins, A. C., and J. M. Dubach. 2001. Nuclear DNA variation in spider monkeys (Ateles). Mol. Phylo. Evol. 19:67-75." 100 2 aldolase A intron nuDNA 466 Neighbor Joining K2P none Chordata 5 -1.935370901 0.071087116 . . . "((chamek:17.8,(hybridus:18.9,robustus:35.5):1.1):16.3,chamek:35.7,paniscus:35.9);" 081_Burridge_1999_MPE "Burridge, C. P. 1999. Molecular phylogeny of Nemadactylus and Acantholatris (Perciformes: Ciffhitoidea: Cheilodactylidae), with implications for taxonomy and biogeography. Mol. Phylo. Evol. 13:93-109." 88 4 "cyt b, d-loop" mtDNA 673 Neighbor Joining K2P 22.1 0.05 0.002262443 substitutions/site 0.0115 Chordata 9 -2.856357332 0.094372892 0.293754443 0.012327382 3.577487994 "((N_macropterus:7.5,A_monodactylus:17.5):6.8,((N_macrodactylus:4.0,A_monodactylus:6.8):7.4,(N_bergi:11.4,((A_monodactylus:9.5,N_macrodactylus:11.3):1.3,(Nemadactylus_sp:13.6,A_gayi:12.5):8.8):2.1):1.0):2.6);" 082_Chesser_etal_2000_MPE "Chesser, R. T. 2000. Evolution in the high Andes: The phylogenetics of Muscisaxicola ground-tyrants. Mol. Phylo. Evol. 15:369-380." 100 2 "COI, ND3" mtDNA 1035 Neighbor Joining 74.7 0.15 0.002008032 substitutions/site 0.0115 Chordata 13 1.456428906 2.055962165 0.288491852 0.007566141 9.355173722 "(((((((albafrons:5.7,cinerea:2.7,rufvertex:5.2):0.1,fluvitucha:3.7):0.1,juvinensis:9.6):0.1,alpina:7.2):6.3,(((albilora:6.4,macloviavea:3.0):2.0,alpina:6.6):1.1,(capistrata:4.7,frontalis:3.6):4.9):3.4):33.5,maculirastris:50.2):4.9,fluviatilis:54.1);" 084_Chippendale_etal_1999_MPE "Chippendale, P. T., V. K. Dave, D. H. Whitmore, and J. V. Robinson. 1999. Phylogenetic relationships of North American damselflies of the genus Ischnura (Odonata: Zygoptera: Coneagrionidae) based on sequences of three mitochondrial genes. Mol. Phylo. Evol. 11:110-121." 93 3 "cyt b, 12S" mtDNA 1205 Neighbor Joining none Arthropoda 15 0.242369562 0.945210027 . . . "(((barberi:38.1,(((((cervula:3.6,gemina:3.2):6.8,erratica:10.2):2.3,((((damula:0.0,perparva:5.0):0.1,verticalis:3.1):3.0,posita:6.8,demorsa:4.8):2.9,denticollis:10.1):6.3):6.8,kellicotti:39.0):8.2,(hastata:35.2,prognatha:28.3):4.3):6.2):3.9,ramburii:37.4):4.9,capreola:63.2);" 086_CortesOrtiz_etal_2003_MPE "Cortes-Ortiz, L., E. Bermingham, C. Rico, E. Rodriguez-Luna, I. Scampaio, and M. Ruiz-Garcia. 2002. Molecular systematics and biogeography of the Neotropical monkey genus, Alouatta. Mol. Phylo. Evol. 26:64-81" 86 5 "cyt b, ATPase 6/8" mtDNA 1642 Maximum Likelihood TrN+G 3.8 0.01 0.002631579 substitutions/site 0.0115 Chordata 9 -1.472241421 0.277321714 0.272638141 0.010618794 4.806922293 "(((A_palliata:1.4,A_coibensis:1.4):8.4,A_pigra:9.6):11.4,((((A_seniculus:7.6,A_sara:7.6):2.8,A_macconelli:10.5):2.1,A_caraya:12.4):3.5,(A_belzebul:12.6,A_guariba:12.7):3.2):5.0);" 087_Crochet_etal_2004_MPE "Crochet, P. -A., O. Chaline, Y. Surget-Groba, C. Debain, and M. Cheylan. 2003. Speciation in mountains: phylogeography and phyolgeny of the rock lizards genus Iberolacerta (Reptilia: Lacertidae). Mol. Phylo. Evol. 30:860-866." 100 2 control region mtDNA 1493 Neighbor Joining K2P+G 1 1 1 Million years Chordata 9 -0.88668282 0.613813776 . . . "((((cantabrica:1.4,monticola:1.4):2.0,martinezricai:3.4):5.1,(cyreni:0.8,castiliana:0.8):7.7):0.0,(((aranica:3.9,bonnali:3.9):0,aurelioi:3.9):4.6,horvathi:8.5):0.0);" 089_Daniels_etal_2002_MPE "Danforth, B. N., H. Sauquet, and L. Packer. 1999. Phylogeny of the Bee genus Halictus (Hymenoptera: Halictidae) based on parsimony and likelihood analyses of nuclear EF-1a sequence data. Mol. Phylo. Evol. 25:511-523" 100 1 "12S, 16S, COI" mtDNA 1253 Maximum Likelihood F81+G 23.9 0.03990423 0.001669633 substitutions/site 0.0115 Arthropoda 14 -2.126247441 0.445163933 0.211496659 0.00372757 6.177097654 "(calcaratus:85.8,((clarus:19.5,depressus:18.1):12.1,((((bayonianus:12.6,(unispinus:3.6,warreni:7.4):8.0):7.7,sidneyi:12.1,(perlatus:2.2,granularis:9.0):16.9):14.0,dentatus:16.8):9.0,lividus:34.9):13.5):15.4,brincki:21.9,parvicorpus:20.8,parvispina:29.5);" 090_de_Queiroz_etal_2002_MPE "Daniels, S. R., B. A. Stewart, G. Gouws, M. Cunningham, and C. A. Matthee. 2002. Phylogenetic relationships of the southern African freshwater crab fauna (Decapoda: Potamonautidae: Potamonautes) derived from multiple data sets reveal biogeographic patterning. Mol. Phylo. Evol. 25: 511-523." 94 2 "cyt b, NADH1,2, 4" mtDNA 3809 Maximum Likelihood GTR+I+G 10.8 0.01 0.000925926 substitutions/site 0.0115 Chordata 32 -2.73158061 0.361931841 0.293828281 0.002877835 7.061719 "(((((A_foxi:44.9,(melanogaster:32.0,validus:62.9):3.2):2.3,(((errans:31.9,exsul:22.0):3.0,scaliger1:39.4):3.2,(godmani:25.4,((mendax:10.0,sumichrasti:15.3):7.4,(scalaris:2.3,scaliger2:1.6):18.2):12.5):3.8):3.4):15.0,(nigronuchalis:53.1,rufipunctatus:51.9):16.2):8.2,((((((((atratus:11.2,elegans:9.2):6.7,(couchii:18.1,gigas:16.0):0.8):10.3,ordinoides:21.0):3.2,hammondil:32.7):3.0,(brachystoma:6.6,(butleri:8.2,radix:2.8):2.4):22.7):5.7,(eques:26.8,marcianus:42.6):17.5):24.3,((cyrtopsis1:50.9,pulchrilatus:28.2):4.4,cyrtopsis2:43.8):27.1):14.3,(chrysocephalus:44.2,fulvus:47.5):20.4):7.3):13.3,((proximus:41.0,sauritus:25.2):54.0,sirtalis:61.7):10.3);" 091_Demastes_etal_2002_MPE "de Queiroz, A., R. Lawson, and J. A. Lemos-Espinal. 2002. Phylogenetic relationships of North Ameican garter snakes (Thamnophis) based on four mitochondrial genes: How much DNA sequence is enough? Mol. Phylo. Evol. 22: 315-329." 100 2 cyt b mtDNA 1133 Maximum Likelihood GTR+I+G 23 0.1 0.004347826 substitutions/site 0.0115 Chordata 14 0.482900943 1.145581621 0.147868626 0.001822094 14.09410416 "((((C_castanops:19.7,C_goldmani:21.2):10.8,C_merriami:19.3):5.8,(((C_gymnurus2:12.9,((C_tylorhinus5:1.5,C_nelectus:1.0):5.2,((C_zinseri:0.9,C_tylorhinus4:1.1):2.9,C_tylorhinus3:2.3):1.9):5.4):2.5,(C_fumosus:1.00,(C_tylorhinus2:4.8,C_gymnurus1:4.8):0.9):11.5):1.9,C_tylorhinus1:24.1):7.7):13.4,P_bulleri:31.6);" 092_Dietrich_etal_1997_MPE "Demastes, J. W., T. A. Spradling, M. S. Hafner, D. J. Hafner, and D. L. Reed. 2002. Systematics and Phylogeography of Pocket Gophers in the Genera Cratogeomys and Pappogeomys. Mol. Phylo. Evol. 22:144-145." 88 4 "16S, ND1-4" mtDNA 1496 Maximum Likelihood TrN 7.2 0.010026738 0.001392602 substitutions/site 0.0115 Arthropoda 37 -1.729738045 0.551137248 0.320504889 0.002934954 7.85234295 "(((((((abbreviata:21.1,((((bandarita:4.1,gila:19.5):1.5,mescalero:2.6):1.5,pectinata:2.3):0.7,collorum:1.6):9.6):3.7,((curvata:1.4,surcula:2.5):5.4,minima:8.5):7.4):11.6,((canyonensis:5.8,zacate:11.7):22.3,doeringae:30.1):7.6):15.7,inflata:33.0):8.3,((((arenicola:11.5,stylata:13.2):5.6,celata:8.4):14.2,((decora:3.6,modica:6.0):15.4,youngi:18.7):7.1):8.5,((arizonensis:32.1,flexulosa:22.5):6.2,(picta:38.6,pyrops:21.4):5.8):11.2):7.3):8.4,((albida:6.6,grammica:7.3):35.5,(species:10.1,serrata:11.5):20.8):11.3):16.8,(areolata:39.7,((((atlantica:22.4,producta:26.2):8.5,(dakota:20.7,graminea:19.3):14.5):7.0,(prariana:21.4,reflexa:26.8):11.7):7.8,((clayi:9.5,sandersi:8.0):3.1,delongi:3.5):15.2):13.1):16.5);" 094_Ducroz_etal_1998_MPE "Dietrich, C. H., R. F. Whitcomb, and W. C. Balck IV. 1997. Phyogeny of the grassland leafhopper genus Flexamia (Homoptra: Cicadellidae) based on Mitochondrial NDA sequences. Mol. Phylo. Evol. 8:139-149." 100 5 cyt b mtDNA 1140 Neighbor Joining 105 6 0.057142857 Million years 1 Chordata 7 -0.459044116 0.305117764 0.242651138 0.011775915 5.307142844 "(((species1:24.9,species2:24.9):33.2,species3:58.0):34.6,((niloticus:38.9,(abyssinicus:11.9,blicki:12.3):27.0):1.8,somalicus:40.8):52.3);" 095_Emerson_etal_1999_MPE "Durcroz, J. -F., V. Volobouev, and L. Granjon. 1998. A molecular perspective on the systematics and evolution of the genus Arvicanthis (Rodentia, Muridae): Inferences from complete Cytochome b gene sequences. Mol. Phylo. Evol. 10:104-117." 88 4 "COI,COII" mtDNA 1614 Neighbor Joining K2P+G 46.3 0.03 0.000647948 substitutions/site 0.0115 Arthropoda 13 -0.223519138 0.910293447 0.567877117 0.029316765 3.20144416 "((((angularis:3.7,appendiculatus:4.6):10.0,canariensis:5.5):26.6,rectus:62.6):3.4,(((((gomerensis:2.4,spretus:5.5):10.4,(marcellae:11.7,(obliteratus:12.6,refleximargo:12.4):2.2):2.3):2.1,pilosipennis:23.1):7.1,(cognatus:14.5,laureticola:25.6):3.1):15.0,abaxoides:73.7):3.8);" 096_Faber&Stepien_1998_MPE "Faber, J. E., and C. A. Stepien. 1998. Tandemly repeated sequences in the mitochondrial DNA control region and phylogeography of Pike-Perches Stizostedion. Mol. Phylo. Evol. 10:310-322." 80 5 control region mtDNA 1262 Neighbor Joining K2P 61.7 3 0.048622366 Million years 1 Chordata 6 -1.999812117 0.113576159 0.366770696 0.033630186 2.266410035 "(((S_vitreum:36.6,S_canadense:23.1):14.6,(S_lucioperca:21.5,S_volgensis:16.5):17.5):9.4,(G_cernuus:27.1,E_zonale:56.4):1.6);" 098_Garb_etal_2004_MPE "Garb, J. E., A. Gonzalez, and R. G. Gillespie. 2004. The black widow spider genus Latrodectus (Araneae: Theridiidae): Phylogeny, biogeography, and invasion history. Mol. Phylo. Evol. 31:1127-1142." 60 3 COI mtDNA 428 Maximum Likelihood GTR+I+G 3.9 0.05 0.012820513 substitutions/site 0.0115 Arthropoda 21 1.203294409 0.856359737 0.085802545 0.000387478 36.09645048 "((geometricus:15.6,rhodesiensis:6.6):12.2,((((((((antheratus:6.4,(corallinus:0.0,sp:0.0,diaguita:0.0):5.8):6.4,mirabilis:1.1):0.8,sp:0.0,mirabilis:0.0,variegatus:0.0):8.5,((mactans:4.7,hesperus:9.2):1.3,(variolus:6.0,bishopi:7.6):2.6):14.4):1.9,(pallidus:5.1,revivensis:8.1):7.0):1.1,menavodi:12.8):1.0,(hasselti:2.5,katipo:4.3):20.8):7.4,(tredecimguttatus:0.0,renivulvatus:1.4):6.7):24.0);" 099_GarciaMoreno_etal_2001_MPE "Garcia-Moreno, J., J. Ohlson, J. Fjedsas. 2001. MtDNA sequences support monophyly of Hemispingus Tanagers. Mol. Phylo. Evol. 21:424-435." 75 2 ND2 mtDNA 310 Maximum Likelihood HKY+G 7.3 0.05 0.006849315 substitutions/site 0.0115 Chordata 30 -2.244660598 0.37039272 0.144694512 0.000747732 14.24691642 "((((((bresilius:2.0,carbo:1.0):4.7,((costaricensis:0.9,passerinii:0.0):2.7,icteronotus:4.2):2.3):3.8,sanguinolentus:11.9):10.8,(((atropileus:8.0,(auricularis:13.2,calophrys:5.0):1.0):1.3,trifasciatus:17.0):1.7,(((melanotis:2.5,frontalis:9.6):4.3,piruae:8.5):4.0,rufosuperciliaris:22.1):4.0,((xantghophthalmus:6.9,verticalis:6.0):5.1,superciliaris:9.8):4.8):17.5):4.6,((canigularis:10.9,((flavigularis:0.0,paravirostris:4.9):2.7,(ophaeocephalus:10.0,sernifuscus:2.0):11.7):0.3):1.7,((((rufinucha:2.7,luviceps:4.3):3.2,latrixichus:5.4):1.1,rufigenis:3.0):9.9,brunneinucha:12.2):3.5):10.2):2.0,(coronatus:13.1,luteoviridis:3.5,nigrocristatus:7.8):8.6);" 100_GraciaMoreno_etal_1999_MPE "Garcia-Moreno, J., P. Arctander, and J. Fjedsas. 1999. A case of rapid diversification in the neotropics:phylogenetic relationship among Cranioleuca Spinetails (Aves, Furnariidae). Mol. Phylo. Evol. 12:273-281." 67 2 "cyt b, ND2" mtDNA 757 Maximum Likelihood HKY+G 31.8 0.1 0.003144654 substitutions/site 0.0115 Chordata 12 -3.845688119 0.120828955 0.883244465 0.078012078 1.104189423 "(((((((marcapatae:2.6,albiceps:3.8):5.6,vulpina:6.0):2.0,((obsoleta:3.2,henricae:1.3):0.9,pyrrhophia:1.3):3.1,albicapilla:4.8):2.2,demissa:4.7):0.7,erythrops:2.8):2.9,(curtata:1.6,antisiensis:1.3):0.5):1.7,baroni:1.4);" 101_Gonzalez_etal_1996_MPE "Gonzalez, P., F. Pinto, M. Nogales, J. Jimenez-Asensio, M. Hernandez, and V. M. Cabrera. 1996. Phylogenetic relationships of the Canary islands endemic lizard genus Gallotia (Sauria: Lacertidae), inferred from nitochondrial DNA sequences. Mol. Phylo. Evol. 6:63-71." 100 5 "12S, cyt b" mtDNA 307 Neighbor Joining 6.5 0.01 0.001538462 substitutions/site 0.0115 Chordata 11 0.43989968 1.326844898 0.224474407 0.005598751 8.212377046 "((((((Ggag:2.7,Ggae:12.3):3.7,Ggap:18.7):9.4,(Ggac:11.7,Ggao:1.8):23.7):9.6,Gsis:45.4):12.2,(Gata:14.5,(Gatl:3.4,Gatd:5.8,Gati:3.4):18.0):33.0):7.9,Gst:62.5);" 102_Groombridge_etal_2004_MPE "Groombridge, J. J., C. G. Jones, R. A. Nichols, M. Carlton, and M. W. Bruford. 2004. Molecular phylogeny and morphological change in the Psittacula parakeets. Mol. Phylo. Evol. 31:96-108." 79 4 cyt b mtDNA 800 Maximum Likelihood HKY+G 101.2 9 0.088932806 Million years 1 Chordata 11 -1.897114335 0.364705188 0.193240406 0.004149095 6.599370035 "(((Slaty_head:39.5,Plum_head:39.5):22.0,Blossom_head:61.5):12.8,((((Derbyan:6.1,Moustached:6.1):37.1,Longtail:43.4):11.6,Maiabar:55.0):11.5,(Alexandine:60.0,((Indian:17.5,Echo:17.5):8.7,African:26.3):33.5):6.3):7.8);" 106_Hardman_2004_MPE "Hardman, M. 2004. The phylogenetic relationships among Noturus catfishes (Siluriformes: Inctaluridae) as inferred from mitochondrial gene cytochrome b and nucleae recombination activating gene 2. Mol. Phylo. Evol. 30:395-408." 100 7 cytb & RAG2 mtDNA & nuDNA Maximum Likelihood TVM+I+G 4.5 0.01 0.002222222 substitutions/site Chordata 26 -3.84240063 0.29551941 . . . "(((((((((((((munitus:4.9,stigmosus:3.8):1.3,placidus:9.4):4.5,eleutherus:12.5):3.7,(furiosus:8.5,flavater:11.6):2.5):6.6,(miurus:18.1,flavipinuis:22.1):1.2):3.4,(alabater:5.2,affalabaster:9.8):9.5):2.1,taylori:20.3):1.2,(((hildebrandi:11.1,baileyi:12.0):3.7,elegans:13.2):2.0,affelegans:10.3):9.4):3.6,(fumebris:12.3,leptacantleus:14.1):17.6):1.3,((broadtail:6.6,insignis:2.5):12.4,flavus:21.8):2.1,gilberti:21.9):3.0,((lachneri:15.2,gyrinus:14.5):10.8,nocturnus:22.7):6.7):0.3,exilis:33.1):2.0,phaeus:29.0);" 107_Harrison_2004_MPE "Harrison, J. S. 2004. Evolution, biogeography, and the utility of mitochondrial 16s and COI genes in phylogenetic analysis of the crab genus Austinixa (Decapoda: Pinnotheridae). Mol. Phylo. Evol. 30:743-754." 100 4 "16S, COI" mtDNA Maximum Likelihood GTR+I+G 22.2 0.1 0.004504505 substitutions/site 0.0115 Arthropoda 8 -1.956014492 0.613422632 0.045386662 0.000343325 20.83823183 "((((((aidae:0,hardyi:1.2):68.7,gorei:49.1):18.1,cristata:30.1):9.5,(behreae:21.1,chacei:14.3):64.3):15.2,felipensis:40.8):11.5,patagoniensis:30.6);" 110_Hodges&Zamudio_2004_MPE "Hodges, W. L. and K. R. Zamudio. 2004. Horned lizard (Phrynosoma) phylogeny inferred from mitochondrial genes and morphological characters: understanding conflicts using multiple approaches. Mol. Phylo. Evol. 31:961-971." 100 1 "cyt b, ND4" mtDNA 2510 Maximum Likelihood TrN+I+G 14.3 0.05 0.003496503 substitutions/site 0.0115 Chordata 13 -3.363309826 0.144159951 0.090117668 0.00073829 13.24763703 "(((((((((ditmarsi:19.7,hernandesi:10.7):5.0,douglasii:16.3):11.1,orbiculare:26.6):5.6,modestum:29.6):5.1,solare:36.8):3.1,((platyrhinos:12.8,mcallii:22.0):17.1,coronatum:29.5):2.8):1.8,(taurus:20.9,braconnieri:21.6):14.0):3.2,comutum:38.7):5.7,asio:41.9);" 112_Ingram_etal_2004_MPE "Ingram, C. M., H. Burda, and R. L. Honeycutt. 2004. Molecular phylogenetics and taxonomy of the African mole-rats, genus Cryptomys and the new genus Coetomys Gray, 1864. Mol. Phylo. Evol. 31:997-1014." 100 4 12S & transthyretin intron mtDNA & nuDNA 2126 Maximum Likelihood GTR+I+G 4 0.01 0.0025 substitutions/site Chordata 10 -0.371439323 0.171123638 . . . "(((whytei:7.5,(((anselli:2.0,micklemi:2.7):3.0,damarensis:4.9):1.3,darlingi:5.1):0.2):1.4,bocagei:4.8):15.8,(hottentotus:11.5,((anomalus:4.8,natalensis:8.4):3.7,holosericeus:7.0):1.2):17.8);" 113_Jordal_etal_2004_MPE "Jordal, B. H., L. R. Kirkendall, and K. Harkestad. 2004. Phylogeny of a Macaronesian radiation: host-plant use and possible cryptic speciation in Liparthrum bark beetles. Mol. Phylo. Evol. 31:554-571." 94 4 COI mtDNA 675 Maximum Likelihood GTR+I+G 0.197 0.05 0.253807107 substitutions/site 0.0115 Arthropoda 15 -3.47733295 0.12663027 0.046032241 0.000162997 28.89487011 "((pinicola:0.859,(nigrescens:1.869,rumicis:0.441):0.04):0.179,((loweri:0.521,curlum:1.242):0.15,((bituberculatum:1.06,(semidegener:0.483,(canum:0.594,arternisae:0.381):0.257):0.479):0.07,((loweanum:0.472,pilosum_A:0.497):0.331,(bicaudatum:0.626,((inarmatum:0.313,pilosum_C:0.558):0.272,pilosum_B:0.43):0.056):0.174):0.179):0.075):0.326);" 114_Joseph_etal_2004_MPE "Joseph, L., T. Wilke, E. Bermingham, D. Alpers, and R. Ricklefs. 2004. Towards a phylogenetic framework for the evolution of snakes, rattles, and rolls in Myiarchus tyrant-flycatchers (Aves: Passeriformes: Tyrannidae). Mol. Phylo. Evol. 31:139-152." 86 1 ATPase6/8 mtDNA 842 Bayesian HKY+G 2.4 0.001187648 0.000494854 substitutions/site 0.0115 Chordata 18 -3.414444494 0.155217663 1.006758949 0.063347724 1.807008986 "((swainsoni:11.2,(cephalotes:24.2,(phaeocephalus:14.0,panamensis:18.0,(ferox:13.8,venezuelenais:12.2):16.6):15.9,((tuberculifer:10.7,barbirostris:14.2):3.4,swainsoni2:14.9):3.1):3.9):19.4,(valvus:23.1,((stolicus:5.7,sangrae:4.2):16.3,((antildarum:8.2,oberi:9.0):8.9,(crinitus:12.5,yucetanensis:24.7,(cinerascens:19.5,tyrannulus:17.6):2.5):5.0):2.8):8.1):17.0);" 115_Kiefer_etal_2002_MPE "Kiefer, A., F. Mayer, J. Kosuch, O. von Helversen, and M. Veith. 2002. Conflicting molecular phylogenies of European long-eared bats (Plecotus) can be explained by cryptic diversity. Mol. Phylo. Evol. 25: 557-566." 100 2 "16S, ND1, D-loop" mtDNA 1714 Neighbor Joining TrN 3.2 0.01 0.003125 substitutions/site 0.0115 Chordata 4 -1.080714101 0.005573722 0.058089976 0.001687223 10.91032609 "((austriacus:23.1,kolombatovici:20.3):22.4,(indet:27.5,auritus:21.9):11.5);" 116_Klicka_etal_2003_MPE "Klicka, J., R. M. Zink, and K. Winker. 2003. Longspurs and snow bunthings: phylogeny and biogeography of a high-latitude clade (Calcarius). Mol. Phylo. Evol. 26:165-175." 100 1B cyt b mtDNA 1143 Maximum Likelihood GTR+I+G 8.7 0.043744532 0.005028107 substitutions/site 0.0115 Chordata 6 -0.307761094 0.919009304 0.050405357 0.000635175 20.05777466 "(((P_hyperboreus:0.6,P_nivalis:1.0):30.9,C_mccownii:30.7):9.2,(C_lapponicus:34.3,(C_ornatus:13.5,C_pictus:15.9):37.1):8.3);" 117_Kochzius_etal_2003_MPE "Kochzius, M., R. Soller, M. A. Khalaf, and D. Blohm. 2003. Molecular phylogeny of the lionfish genera Dendrochirus and Pterois (Scorpaenidae, Pteroinae) based on mitochondrial DNA sequences. Mol. Phylo. Evol. 28:396-403." 54 2 "cyt b, 16S" mtDNA 964 Neighbor Joining K2P 4.5 0.01 0.002222222 substitutions/site 0.0115 Chordata 7 -0.63815879 0.421319469 0.19039737 0.007250232 6.254226428 "((brachypterus:28.8,((zebra:9.8,(orntennates:3.4,membransae:2.5):13.7):3.0,radiata:21.1):2.4):12.8,(miles:12.1,volatus:10.7):15.6);" 119_Kosuch_etal_2001_MPE "Kosuch, J., M. Vences, A. Dubios, A. Ohler, and W. Bohme. 2001. Out of Asia: Mitocondrial DNA evidence for an oriental origin of tiger frogs, genus Hoplobatrachus. Mol. Phylo. Evol. 21:398-407. " 100 1 16S mtDNA 572 Neighbor Joining HKY+G 3.3 0.05 0.015151515 substitutions/site 0.0115 Chordata 4 -0.510112184 0.247830891 0.029475728 0.000434409 23.40250306 "(((H_chinensis:9.3,H_tigerinus:5.0):1.0,H_crassus:9.5):7.3,H_occipatalis:19.4);" 120_Lavery_etal_2004_MPE "Lavery, S., T. Y. Cahn, Y. K. Tam, and K. H. Chu. 2004. Phylogenetic relationships and evolutionary History of shrimp genus Penaeus s.l. derived from mitochondrial DNA. Mol. Phylo. Evol. 31:39-49." 93 3 "COI, 16S" mtDNA 888 Maximum Likelihood GTR+I+G 3.3 0.01 0.003030303 substitutions/site 0.0115 Arthropoda 24 -1.741023339 0.414018956 0.135480732 0.000834319 16.64227174 "(((((((aztecus:9.6,paulensis:16.2):1.9,subtilis:12.7):6.7,brasiliensis:16.3):1.5,(atrorurum:2.2,notialis:1.3):14.7):12.5,((styulinostris:18.6,vannamej:14.2):3.0,setiferus:33.5):11.9):23.7,(((chimensis:22.8,((indicus:6.5,(penicilanes:1.3,silasi:2.6):4.9):4.3,merguiensis:1.5):18.6):13.4,(semisulcatus:27.9,esculentus:31.3):9.4):2.1,monodon:42.4):2.5):23.8,((((japonicus:17.8,canalliculatus:17.4):4.3,((latisulcatus:17.1,plebejus:18.0):6.6,longistylus:14.8):5.5):10.5,marginatus:33.7):5.0,kerarhurus:36.6):13.8);" 121_Lee_etal_2003_MPE "Lee, S., C. S. Parr, Y. Hwang, D. P. Mindell, and J. C. Choe. 2003. Phylogeny of magpies (genus Pica) inferred from mtDNA data. Mol. Phylo. Evol. 29:250-257." 100 4 "16S, ND1" mtDNA 813 Neighbor Joining K2P 9.3 0.01 0.001075269 substitutions/site 0.0115 Chordata 5 -0.443609023 0.484084154 0.482481121 0.077596011 1.874708126 "(((camtschatica:5.9,pica:4.4):6.9,(hudsonia:6.2,nuttalli:8.5):8.4):6.5,sericea:19.7);" 122_Lucchini_etal_2001_MPE "Lucchini, V., J. Hoglund, S. Klaus, J. Swenson, and E. Randi. 2001. Historical biogeography and a mitochondrial DNA phylogeny of Grouse and Ptarmigan. Mol. Phylo. Evol. 20:149-162." 100 3 "12S, 16S, ND2, cyt b, control region" mtDNA 2690 Maximum Likelihood TrN+G 8.9 0.01 0.001123596 substitutions/site 0.0115 Chordata 17 -2.235078698 0.341337729 0.270337969 0.004872174 6.233057212 "(((bonasia:19.2,sewerzowi:43.1):37.3,umbellus:42.7):12.0,(((canadensis:31.0,falcipennis:25.6):20.7,((mlokosiewiczi:15.3,tetrix:15.1):15.4,(parvirostrus:21.0,urogallus:15.7):8.8):10.2):5.3,(((lagopus:15.7,mutus:18.0):15.0,leucurus:26.2):7.0,(urophasianus:40.3,(obscurus:24.3,((cupido:2.6,pallidicintus:2.2):4.6,phasianellus:14.3):29.5):7.6):6.5):2.0):13.7);" 125_Mahoney_2001_MPE "Mahoney, M. J. 2001. Molecular systematics of Plethodon and Aneides (Caudata:Plethodontidea: Plethodontini): Phylogenetic analysis of and old rapid radiation. Mol. Phylo. Evol. 18:174-188." 86 6 ND4 mtDNA 657 Maximum Likelihood HKY+G none Chordata 25 -2.734285194 0.412707433 . . . "((((A_aeneus:55.6,(((A_ferreus:21.4,A_flavipunctatus:33.0):5.1,A_lugubris:28.5):7.1,A_hardii:32.4):8.9):11.9,((((((cinereus:2.0,hoffmani:2.9):9.6,richmondi:10.5):5.7,serratus:18.4):13.6,(((((((fourchensis:6.1,(jordani:11.5,onachitae:9.1):1.9):1.5,teyahalee:13.2):2.0,yonak:19.4):0.1,petraeus:12.6):3.0,glutinosus:6.1):10.7,wehrlei:21.8):2.0,welleri:22.8):4.2):34.9,(dunni:19.5,vehiculum:9.2):11.5):1.3,(elongatus:9.0,stormi:7.0):20.5):2.2):4.3,(larselli:29.9,vandykei:41.6):11.1):2.0,neomexicanus:31.5);" 126_Malhotra&Thorpe_2000_MPE "Malhortra, A., and R. S. Thorpe. 2000. A phylogeny of the Trimeresurus group of pit vipers: New evidence from mitochondrial gene tree. Mol. Phylo. Evol. 16:199-211." 70 3 cyt b mtDNA 660 Maximum Likelihood 22.7 0.1 0.004405286 substitutions/site 0.0115 Chordata 13 -1.884061839 0.361728653 0.098373398 0.000879757 14.41504149 "(((((albolabris:16.0,((purpureonaculatus:3.8,erythrurus:1.5):3.5,cantori:6.6):1.6):24.6,stejnegeri:23.8):0.8,kanburiensis:23.6):4.9,(popeiorum:21.7,(hageni:13.3,flavomaculatus:22.6):11.5):1.9):2.5,(((trigonocephalus:10.3,gramineus:13.9):4.5,malabaricus:23.5):13.1,borneensis:37.9):7.4);" 127_Malone_etal_2000_MPE "Malone, C. L., T. Wheeler, J. F. Taylor, and S. K. Davis. 2000. Phylogeopraphy of the Caribbean rock iguana (Cyclura): Implications for conservation and insights on the biogeopraphic history of the west Indies. Mol. Phylo. Evol. 17:269-279." 100 2 ND4 mtDNA 903 Maximum Likelihood GTR+I+G 1.2 0.011074197 0.009228498 substitutions/site 0.0115 Chordata 9 -1.212365221 0.365166898 0.104592082 0.001562786 12.42837937 "((((((nubila:3.3,cychlura:3.9):0.7,nubila:3.1):3.2,rileyi:2.4):5.4,collei:10.2):3.0,((ricordi:5.1,carinata:5.6):7.3,corinata:9.2):4.1):5.8,pinguis:11.1);" 128_Masta_etal_2002_MPE "Masta, S. E., B. K. Sullivan, T. Lamb, and E. J. Routman. 2002. Molecular systematics, hybridization, and phylogeography of the Bufo americanus complex in eastern North America. Mol. Phylo. Evol. 24:302-314." 57 3 "ND1, 16S" mtDNA 1110 Maximum Likelihood HKY+J117+I+G 2 0.000900901 0.00045045 substitutions/site 0.0115 Chordata 5 -1.282958199 0.10695208 0.492540685 0.080865442 1.602035217 "((americanus:28.8,woodhousii:20.7):12.0,((fowleriS:17.2,terrestris:14.0):24.0,fowleriN:27.1):11.7);" 132_Misof_etal_2000_MPE "Misof, B., C. L. Anderson, and H. Hadrys. 2000. A phylogeny of damselfly genus Calopteryx (Odonata) using mitochondrial 16S rDNA markers. Mol. Phylo. Evol. 15:5-14." 53 3 16S mtDNA 546 Neighbor Joining HKY+I+G 30.1 0.1 0.003322259 substitutions/site 0.0115 Arthropoda 10 -1.043749734 0.408051708 0.200976149 0.005048927 7.516610988 "((M_basilaris:13.1,atrata:17.9):18.7,(((xanthostoma:1.0,splendens:2.4):7.0,(virgo:6.0,haemorrhoidalis:1.3):2.5):7.1,(cornealia:11.2,(maculata:9.5,(dimidiata:22.2,aequabilis:6.2):1.3):8.8):1.7):1.6);" 134_Miya&Nishida_1998_MPE "Miya, M., and M. Nishida. 1998. Molecular phylogeny and evolution of the deep-sea fish genus Sternoptyx. Mol. Phylo. Evol. 10:11-22." 100 7 "12S, 16S" mtDNA 935 Maximum Likelihood TrN+G 27.7 0.05 0.001805054 substitutions/site 0.0115 Chordata 4 0.371641704 0.665185183 0.151330179 0.011450412 5.150289946 "(pseudodiaphana:26.9,(diaphana:8.9,(pseudobscura:1.9,obscura:13.8):4.7):28.0);" 136_Montiero&Pierce_2001_MPE "Monteiro, A., and N. E. Pierce. 2001. Phylogeny of Bicyclus (Lepidoptera:Nympalidae) inferred from COI, COII and EF-1a gene sequence. Mol. Phylo. Evol. 18:264-281." 68 6 "COI, COII" mtDNA 1914 Maximum Likelihood GTR+I+G 103.5 50 0.483091787 Million years 1 Arthropoda 54 -3.217820716 0.616141221 0.064949014 8.11226E-05 31.8781451 "((((alboplagus:0.0,xeneoides:0.0):7.4,xeneas:7.4):29.4,evadne:37.0):29.0,((((analis:1.6,uniformis:1.6):25.1,((hyperanthus:14.1,sciathis:14.1):1.2,procorus:15.3):11.3):28.8,((((((graueri:1.5,sebetus:1.5):8.6,(italus:1.0,zinebi:1.0):9.0):6.9,iccius:17.2):3.4,sweadneri:20.4):17.2,medontias:37.8):8.0,hewitsoni:45.9):9.9):3.5,(((((((((angulosus:9.9,campus:9.9):18.4,anynana:28.5):5.0,mollitia:33.2):3.3,(auricrudus:12.7,(henia:6.0,maridanes:6.0):6.9):23.6):10.1,(mesogenus:21.6,sangmelinae:21.6,sambulos:21.6):24.8):0.4,(((((dorothea:1.1,moyses:1.1):1.7,jefferyi:2.8):16.2,vulgaris:19.0):18.6,sandace:37.7):9.1,ena:46.1,technatis:46.1,vansoni:46.1):0.2):6.4,((((((buea:10.6,sanaos:10.6):14.2,persimilis:24.8):11.8,(((golo:18.6,smithi:18.6):2.3,madetes:21.1):14.2,(istaris:4.5,sophrosyne:4.5):30.9):1.3):0.8,matuta:37.4):6.6,(dubius:41.6,funebris:41.6):2.5):7.5,(cotterelli:31.6,safitza:31.6):20.0):1.4):2.1,((anisops:33.6,dentatus:33.6):18.3,taenias:51.7):3.8):2.7,(ignobilis:45.2,pavonis:44.9):13.0,trilophus:58.1):0.8):7.1);" 137_Moriarty&Cannatella_2004_MPE "Moriarty, E. C., and D. C. Cannatella. 2004. Phylogenetic relationships of the North American chorus frogs (Pseudacris: Hylidae). Mol. Phylo. Evol. 30:409-420." 100 2 "12S, 16S" mtDNA 2400 Maximum Likelihood GTR+I+G none Chordata 17 0.029914535 0.677262012 . . . "((cadaveriria:0.459,regilla:0.456):0.445,((ornata:0.57,(streckeri:0.105,illinoiensis:0.051):0.489):0.45,((occularis:0.588,crucifer:0.635):0.393,((bremleyi:0.153,brachyphona:0.226):0.209,(((nigrita:0.241,feriarum:0.186):0.105,(kalmi:0.072,(triseriata:0.094,feriarum:0.111):0.06):0.111):0.096,(maculata:0.086,triseriata:0.074,clarkii:0.072):0.168):0.125):0.281):0.16):0.286);" 139_Morrison_etal_2004_MPE "Morrison, C. L., R. Rios, and J. E. Duffy. 2004. Phylogenetic evidence for an ancient rapid radiation of Caribbean sponge-dwelling snapping shrimps (Synalpheus). Mol. Phylo. Evol. 30:563-581." 100 2 "COI, 16S" mtDNA 1067 Bayesian GTR+I+G 0.194 0.05 0.257731959 substitutions/site 0.0115 Arthropoda 27 -4.984739186 0.139145335 0.080153859 0.000256986 16.7954743 "(((agelas:0.352,androsi:0.691):0.054,((bousfieldi:0.358,brooksi:0.581):0.12,(banfield:0.244,chacel:0.174):0.311):0.107):0.066,(((anasinuns:0.923,(occidentalis:0.408,((goodei:0.252,longicarpus:0.369):0.048,((panddionis_small:0.349,longicarpus_small:0.378):0.048,(pandiornis_giant:0.13,pandionis:0.107):0.233):0.057):0.049):0.051):0.2,((brevifrons:0.647,(sanciithomae:0.391,williamsi:0.318):0.238):0.117,(((filidigitus:0.379,regatis:0.362):0.16,(rathburae_A:0.299,rathburnae:0.251):0.232):0.369,(herricki:0.64,peciniger:0.507):0.121):0.096):0.01):0.091,((gambarelloides:0.462,(intermediate:0.5,paranepiunsis:0.468):0.186):0.038,mcclendoni:0.564):0.042):0.025);" 140_Murphy&Collier_1999_MPE "Murphy, W. J., and G. E. Collier. 1999. Phylogenetic relationship of African Killifishes in the genera Aphyosemion and Fundulopanchax inferred from mitochondrial DNA sequences. Mol. Phylo. Evol. 11:351-360." 100 2 "cyt b, 12S" mtDNA 785 Neighbor Joining K2P 37.3 0.05 0.001340483 substitutions/site 0.0115 Chordata 49 -4.761646665 0.239711506 0.302814491 0.001950992 6.414204325 "((((((((((A_elegans:2.7,A_cognatum:6.0):1.2,A_decorensei:6.0):0.8,A_cognatum:4.3):4.8,A_melanopteron:16.5):1.0,(A_christyi:12.6,(A_elegans:15.7,(A_rectogoense:17.3,A_lamberti:15.4):3.1):1.6):4.1):18.4,(A_labarrei:24.6,((A_wildekampi:15.4,A_punctatum:18.0):10.2,(A_mimbon:20.2,(A_maculatum:12.6,A_cameroonense:9.4):5.1):15.5):2.1):4.2):1.8,(F_kunzi:45.9,(A_coeleste:23.0,(A_citrinepinnis:25.5,(A_occellatum:15.3,A_aureum:14.8):5.5):9.7):6.1):3.1):9.5,((A_gabunense:23.2,A_striatum:25.0):17.5,((A_exigoideum:11.3,A_primigenium:9.1):26.0,(A_louoessense:24.1,A_ogoense:23.3):17.8):3.0):7.7):3.0,(((A_ahli:21.1,A_australie:24.1):3.2,(A_calliunum:18.7,A_celiae:26.7):3.6):10.8,(((A_bualanum:12.1,A_exiguum:12.0):35.6,A_cyanostictum:52.7):9.1,(A_sp:42.4,(A_bivittatum:20.0,A_volcanum:16.0):14.7):13.6):2.5):1.0):14.9,((F_saneaisabellae:11.1,F_scheeli:10.1):29.7,(((F_filamentosum:26.1,F_robertsoni:33.1):3.5,F_walkeri:32.5):10.1,(((F_deltaense:6.2,F_gulare:8.1):21.6,(F_schwoideri:24.1,F_arneiti:18.8):5.5):6.0,(F_sjoestedi:27.0,(F_gardneri:28.3,(F_mirabile:27.3,F_ndianum:24.5):3.6):3.4):2.2):2.9):3.0):3.6);" 141_Omland_etal_1999_MPE "Omland, K .E., S. M. Lanyon, and S. J. Fritz. 1999. A molecular phylogeny of the new world Orioles (Icterus): the importance of dense taxon sampling. Mol. Phylo. Evol. 12:224-239." 100 7 "cyt b, ND2" mtDNA 2005 Maximum Likelihood K2P 45.8 0.061 0.001331878 substitutions/site 0.0115 Chordata 25 -4.388180464 0.147061455 0.305721765 0.00406373 5.191805817 "(((((((((cayanensis:20.9,(dominicensis:20.6,oberi:12.6,laudabilis:17.1):1.6):2.2,bonana:14.8):2.9,dominicensis:25.1):1.9,(spurius:32.7,dominicensis:22.6):6.3):3.4,cucullatus:27.8):4.6,wagleri:38.1):6.8,maculialatus:32.9):0.9,(((jamacaii:18.1,icterus:15.1):12.0,(graceannae:23.0,pectoralis:22.8):8.2):0.9,mesomelas:37.1):8.1):2.7,((((gularia:13.9,nigrogularis:12.3):5.3,auratus:13.8):2.8,leucopteryx:20.4,pustulatus:20.8,galbula:22.7):17.1,((chrysater:7.4,graduacauda:6.5):19.0,parisorum:29.0):4.6):11.5);" 143_Palma_etal_2002_MPE "Palma, R. E., E. Rivera-Milla, T. L. Yates, P. A. Marquet, and A. P. Meynard. 2002. Phylogenetic and biogeographic relationships of the mouse opossum Thylamys (Didelphimorphia, Didelphidae) in south America. Mol. Phylo. Evol. 25:245-253." 83 3 cyt b mtDNA 1000 Neighbor Joining HKY 20.2 0.05 0.002475248 substitutions/site 0.0115 Chordata 5 -2.855987678 0.002520339 0.053669608 0.000960142 11.38075983 "((((pallidior:46.3,elegans:50.1):25.9,venusta:43.7):19.3,pusilla:49.1):10.1,macrura:32.0);" 145_ParraOlea_2002_MPE "Parra-Olea, G. 2002. Molecular phylogenetic relationships of noetropical salamanders of the genus Pseudoeurycea. Mol. Phylo. Evol. 22:234-246." 79 3 "cyt b, 16S" mtDNA 1113 Maximum Likelihood GTR+I+G 11.7 0.05 0.004273504 substitutions/site 0.0115 Chordata 22 -1.918033395 0.419705738 0.201969389 0.002039582 9.591674569 "(((((juarezi:0.4,saltator:0.0):13.2,unguidentis:13.8):2.4,((Lineatriton:11.5,(werleri:14.8,mystax:10.6):5.2):2.4,(Lineatriton:14.2,(leprosa:17.9,lynchi:8.6):5.4):4.9):3.5):1.4,((sp3:4.5,smithii:8.2):3.3,((((longicauda:4.0,(robertsi:2.2,altamontana:1.3):0.7):0.1,sp2:8.0):0.1,tenchalli:5.6):0.1,melanomolga:5.3,cochranae:6.1):2.6):6.8):4.2,((galeanae:18.7,cephalica:15.7):4.4,(gigantea:8.2,bellii:8.0):11.8):8.4);" 146_Passamonti_etal_2004_MPE "Passamoni, M., B. Mantovani, and V. Scali. 2004. Phylogeny and karyotype evolution of the Iberian Leptynia attenuata species complex (Insecta Phasmatodea). Mol. Phylo. Evol. 30: 87-96." 100 3 COII mtDNA 639 Neighbor Joining TrN+I+G 59.4 23.31 0.392424242 Million years 1 Arthropoda 6 -0.892514587 0.301080663 0.050286385 0.00063218 22.90776513 "(species:58.2,(caprai:22.7,(attenuata2:21.0,attenuata1:21.0,attenuata3:21.0,montana:21.0):2.2):35.6);" 148_Pondella_etal_2003_MPE "Pondella, D. J., M. T. Craig, and J. P. C. Franck. 2003. The phylogeny of Paralabrax (Perciformes: Serranidae) and allied taxa inferred from partial 16S and 12S mitochondrial ribosomal DNA sequences. Mol. Phylo. Evol. 29:176-184." 100 2 "12S, 16S" mtDNA 994 Neighbor Joining 5.9 0.01 0.001694915 substitutions/site 0.0115 Chordata 9 -2.838616998 0.103248264 0.751701511 0.080722166 1.433922654 "(((P_loro:6.4,(P_caliaensis:4.3,P_dewegeri:2.8):3.0,P_albomaculatus:9.0):0.7,P_humeralis:6.5):2.7,((P_auroguttatus:4.0,P_clathratus:4.0):1.5,(P_maculatofasciatus:8.2,P_nebulifer:6.6):1.5):2.3); " 149_Porter_etal_2002_MPE "Porter, B. A., T. M. Cavender, and P. A. Fuerst. 2002. Molecular pholgeny of the snubnose darters, subgenus Ulocentra (genus Etheostoma, family Percidae). Mol. Phylo. Evol. 22:364-374." 89 5 "control region, 12S" mtDNA 1033 Neighbor Joining K2P 15.2 0.01 0.000657895 substitutions/site 0.0115 Chordata 31 -3.627032368 0.243974187 0.772427145 0.020573921 2.468583944 "((lynceum:12.5,zonale:9.1):24.5,(((thalassinum:21.2,(swannanoa:28.5,inscriptum:20.9):0.5):8.0,(rupestre:20.5,(blennioides:16.3,blennius:18.0):2.3):9.0):3.4,((histrio:24.7,(baileyi:26.2,((barrenense:2.3,rafinesquei:7.8):16.8,(simoterum:28.5,atripinne:14.8):17.7):6.7):3.9):3.4,((coosae1:20.0,(coosae2:15.9,scotti:21.8):2.9):12.0,((duryi:15.6,flavum:15.0):9.4,(etnieri:18.6,((zonistium:2.6,pyrrhogaster:15.0):10.3,((raneyi:23.2,(bellator1:0,chermocki:4.4):9.5):2.3,((bellator2:9.8,colorosum:6.0):0.8,(lachneri:8.2,(ramseyi:14.6,(tallapoosae:11.2,brevirostrum:21.4):1.6):1.8):0.7):3.6):1.3):1.1):16.1):1.8):6.9):5.7):13.2);" 150_Randi_1996_MPE "Randi, E. 1996. A mitochondrial cytochrome B phylogeny of the Alectoris partridges. Mol. Phylo. Evol. 6:214-227." 100 6 cyt b mtDNA 1143 Neighbor Joining p-dist 109.2 0.06 0.000549451 substitutions/site 0.0115 Chordata 7 -2.474654341 0.078509854 0.291017559 0.016938244 3.072595687 "(((((chukar:37.8,(philbyi:23.7,magna:42.9):7.2):6.7,graeca:44.5):7.0,rufa:46.3):14.2,barbara:64.8):3.8,melanocephala:60.7);" 151_Randi_etal_2001_MPE "Randi, E., V. Lucchini, A. Hennache, R. T. Kimball, E. L. Braun, and D. Ligon. 2001. Evolution of the mitochondrial DNA control region and cytochrome b genes and the inference of phylogenetic relationships in Avian genus Lophura (Galliformes). Mol. Phylo. Evol. 19:187-201." 91 4 "cyt b, control region" mtDNA 2288 Maximum Likelihood HKY+G 2.5 0.004370629 0.001748252 substitutions/site 0.0115 Chordata 10 -2.156930251 0.373367084 0.090600198 0.001026049 12.23325085 "((((bulweri:61.8,(((edwardsi:3.7,hatinhensis:6.7):30.8,swinholi:39.2):41.8,(leucomelanos:27.0,nycthemera:40.7):37.2):9.1):9.1,inomata:65.2):11.8,erythrophthalma:73.0):7.5,(diardi:48.7,ignita:39.7):30.0);" 152_Reed_etal_2001_MPE "Reed, D. L., M. J. deGravelle, and K. E. Carpenter. 2001. Molecular systematics of Selene (Perciformes: Carangidae) based on cytochrome b sequences. Mol. Phylo. Evol. 21:468-475." 100 2 cyt b mtDNA 1140 Maximum Likelihood GTR+I+G 10.6 0.043859649 0.004137703 substitutions/site 0.0115 Chordata 7 -0.868858433 0.387159455 0.179426716 0.006438789 6.550613499 "(((((peruviana:3.9,setapinnis:5.5):1.3,dorsalis:2.7):8.3,brownii:10.8):3.3,(vomer:7.0,brevoortii:7.8):4.0):10.5,orstedii:12.7);" 153_Ribas&Miyaki_2004_MPE "Ribas, C. C., and C. Y. Miyaki. 2004. Molecular systematics in Aratinga paraleets: species limits and historical biogeography in the 'solstitialis' group, and the systematic position of the Nandayus nenday. Mol. Phylo. Evol. 30:663-675." 60 3 "12S, 16S, cyt b, control region" mtDNA 2029 Maximum Likelihood TrN+I+G 7.7 0.01 0.001298701 substitutions/site 0.0115 Chordata 7 -0.0507305 0.540282486 0.205834543 0.008473572 6.248939839 "((((solstitialis:6.2,(jandaya:5.0,auricapilla:6.3):3.5):5.7,N_nenday:20.5):19.1,weddellii:39.8):12.0,(aurea:29.5,cactorum:43.0):24.5);" 155_RochaOlivares_etal_1999_MPE "Rocha-Olivares, A., R. H. Rosenblatt, and R. D. Vetter. 1999. Molecular evolution, systematics, and zoogeography of the rockfish subgenus Sebastomus (Sebastes, Scorpaenidae) based on mitochondrial cytochrome b and control region sequences. Mol. Phylo. Evol. 11:441-458." 100 7 "cyt b, control region" mtDNA 1633 Maximum Likelihood TrN 123.7 0.64 0.005173808 Million years 1 Chordata 14 -1.633797472 0.376424262 2.560581608 0.546381514 0.638431739 "((((spinorbis:43.6,exsul:43.6):29.9,(notius:58.3,(constellatus:32.1,capensis:32.1):26.2):15.2):15.7,(umbrosus:44.6,lentiginosus:44.6):44.6):33.9,(rosaceus:115.9,(ensifer:71.1,(helvomaculatus:57.1,(simulator:48.8,(rosenblatti:15.5,(eos:9.4,chlorostictus:9.4):6.1):33.2):8.3):14.0):44.8):7.8);" 157_Rubinoff&Sperling_2002_MPE "Rubinoff, D. and F. A.H. Sperling. 2002. Evolution of ecological traits and wing morphology in Hemileuca (Saturniidae) based on a two-gene phylogeny. Mol. Phylo. Evol. 25:70-86." 63 6 COI & EF1-alpha mtDNA & nuDNA 1556 Maximum Likelihood HKY+I+G 6.3 0.009640103 0.001530175 substitutions/site Arthropoda 22 -0.935946833 0.365799119 . . . "((((stonei:16.3,grotei:21.9):8.6,(((nevadensis:3.3,(maia:3.3,BBM:3.2):3.0):18.3,(burnsi:23.3,(neumogeni:11.5,juno:6.6):13.5):1.9):3.1,((((clio:3.1,mojavensis:3.5):0.6,rubra:1.6):1.0,electra:1.8):3.8,ColoradoDesertPopulations:9.0):19.8):1.5):4.5,((nuttalli:14.2,(hera:7.6,eglanterina:15.1):5.5):7.0,(chinatiensis:13.4,griffini:9.7):14.1):5.7):5.6,(((penninsularis:7.7,tricolor:11.8):6.6,hualapai:13.8):3.1,oliviae:16.5):39.5);" 159_Russello&Amato_2004_MPE "Russello, M. A., and G. Amato. 2004. A molecular phylogeny of Amazona: implications for neotropical parrot biogeography, taxonomy, and consercation. Mol. Phylo. Evol. 30:421-437." 94 2 "COI, 12S, 16S & b-fibint7, RP40, TROP" mtDNA & nuDNA 3160 Maximum Likelihood GTR+I+G 6.9 0.005 0.000724638 substitutions/site Chordata 27 -1.61737255 0.55820268 . . . "(((((((((A_aestiva:3.9,A_ochrocephala3:0):6.8,((A_auropalliata:1.8,A_oratrix:4.5):1.5,ochrocephala2:2.0):2.0):0.8,A_barbadensis:3.8,A_ochrocephala1:4.8):2.3,(A_arausiaca:5.3,A_versicolor:5.8):2.8):13.8,(A_dufresniana:7.8,A_rhodocorytha:6.4):19.4):1.6,(A_farinosa:24.3,A_kawalli:16.4):2.7):3.4,(((A_amazonica:6.5,A_guildingii:10.7):2.0,A_brasiliensis:8.6):8.5,A_imperialis:21.0):6.3):0.8,(A_festiva:21.2,((A_pretrei:5.7,A_tucumana:4.0):10.2,A_vinacea:17.6):4.3):1.5):1.6,((A_agilis:19.0,(A_collaria:5.7,((A_leucocephala:3.9,A_vittata:5.3):0.9,A_ventralis:0.5):4.0):7.7):1.5,A_albifrons:14.0):6.9);" 160_SalazarBravo_etal_2001_MPE "Salazar-Bravo, J., J. W. Dagoon, D. S. Tinnin, and T. L. Yates. 2001. Phylogeny and evolution of the neotropical rodent genus Calomys: Inferences from mitochondrial DNA sequence data. Mol. Phylo. Evol. 20:173-184." 100 4 cyt b mtDNA 1140 Maximum Likelihood GTR+I+G 81 10 0.12345679 Million years 1 Chordata 10 0.013887496 0.805574976 0.174946004 0.003825763 8.808641967 "((((((innom:0,fecundus:0):1.8,callosus:1.6):9.0,venustus:10.7):41.8,(laucha:45.2,tener:45.2):7.3):8.8,hummelincki:61.2):10.0,(sorellus:34.7,(lepidus:21.5,musculinus:21.5):13.5):36.6);" 161_Schauble_etal_2000_MPE "Schauble, C. S., C. Mortiz, and R. W. Slade. 2000. A molecular phylogeny for the frog genus Limnodynastes (Anura: Myobatrachidae). Mol. Phylo. Evol. 16:379-391." 100 3 "16S, ND4" mtDNA 820 Maximum Likelihood HKY+J142+I+G 1 1 1 substitutions/site 0.0115 Chordata 16 -0.728537623 0.630033228 0.078799651 0.000443528 24.08559783 "((brevis:0.207,(ornatus:0.057,spenceri:0.087):0.252):0.049,((((M_lingerius:0.105,convexiusculus:0.09):0.036,salmini:0.099):0.059,(((depressus:0.177,fletcheri:0.064):0.042,terminaiensis:0.157):0.025,peronii:0.144):0.047):0.017,(dorsalis:0.040,(((dunerlli:0.001,interioris:0.001):0.013,insularis:0.017):0.036,(grayi:0.034,terraetrginae:0.028):0.018):0.015):0.080):0.068);" 162_Scott_etal_2004_MPE "Scott, I. A.W., J. S. Keogh, and M. J. Whiting. 2004. Shifting sands and shifty lizards:molecular phylogeny and biogeography of African flat lizards (Platysaurus). Mol. Phylo. Evol. 31:618-629." 93 2 ND4 mtDNA 864 Maximum Likelihood GTR+I+G 9.3 0.05 0.005376344 substitutions/site 0.0115 Chordata 14 -2.885783166 0.133350496 0.075077501 0.000469719 18.9685963 "(((broadleyi:14.0,capensis:6.3):14.3,(((imperator:23.9,torquatus:24.6):8.4,rhodesianus:24.7):14.4,(((((intermedius:13.0,monotropis:14.7):4.0,minor:13.4):2.4,nigrescens:17.0):6.2,(lebornoensis:14.5,wilhelmi:12.0):16.7):1.7,orientalis:15.1):6.2):5.7):13.9,(mitchelli:25.7,maculatus:30.5):6.3);" 163_Serb_etal_2003_MPE "Serb, J. M., J. E. Buhay, and C. Lydeard. 2003. Molecular systematics of the north American freshwater bivalve genus Quadrula (Unionidae: Ambleminae) based on mitochondrial ND1 sequences. Mol. Phylo. Evol. 28:1-11." 85 3 ND1 mtDNA 658 Maximum Likelihood p-dist 3 0.015197568 0.005065856 substitutions/site 0.0115 Mollusca 20 -0.971191952 0.654847067 0.275768628 0.004224908 6.701418543 "(((((((((aurea:1.2,pustulosa:1.7):1.8,mortoni:2.8,refulgens:1.0):0.9,F_succissa:4.3):3.0,(nodulata:3.8,petrina:6.1):2.7):5.1,Q_infucata:9.2):3.5,(asperata:1.0,keineriana:0.8):7.3):2.9,(((intermedia:10.8,metanevra:8.6):1.6,sparsa:4.2):4.3,cylindrica:12.5):5.4):2.9,((rumphiana:2.9,quadrula2:1.7):1.4,apiculata:1.6):8.4):3.4,((nobilis:1.9,quadrula1:0.5):7.6,T_verrucosa:9.2):3.1);" 165_Sipes&Wolf_2001_MPE "Sipes, S. D., and P. G. Wolf. 2001. Phylogenetic relationships within Diadasia, a group of specialist bees. Mol. Phylo. Evol. 19:144-156." 61 3 COI/COI mtDNA 1845 Maximum Likelihood GTR+I+G 10.8 0.027100271 0.002509284 substitutions/site 0.0115 Arthropoda 28 -4.294499157 0.150268371 0.208104695 0.001665676 8.500071699 "(((((((((((consociata:6.9,martinalis:6.9):2.7,nitidifrons:8.2):2.2,martialis:7.0):5.4,(diminuta:11.3,lutzi:12.7):2.8):6.4,(bituberculata:13.9,laticauda:16.1):6.0):6.5,megamorpha:24.8):4.6,((nigrifrons:11.7,palmarum:13.4):6.8,tuberculifrons:13.7):3.2):5.0,((((allfictula:17.9,vallicola:17.1):4.8,sphaeraloearum:21.9):6.0,angusticeps:14.1):11.2,afflicta:17.8):5.4):4.9,(((knabiana:11.6,opuntiae:9.8):5.8,piercei:13.1):4.8,(australis:16.8,rinconis:16.8):0.1):7.5):7.9,enavata:28.8):5.2,(((baeri:14.8,hirta:11.3):14.4,chilensis:15.9):10.0,(ochracea:28.7,pereyrae:16.8):6.4):8.7);" 168_Stone&Cook_2002_MPE "Stone, K. D., and J. A. Cook. 2002. Molecular evolution of Holarctic martens (genus Martes, Mammalia: Carnivora: Mustelidae). Mol. Phylo. Evol. 24:169-179." 100 1 cyt b mtDNA 1140 Maximum Likelihood TrN+I+G 2.8 0.01 0.003571429 substitutions/site 0.0115 Chordata 8 -0.148036448 0.801969565 0.143303492 0.003422648 9.49340176 "(((((M_americana:10.8,M_foina:20.9):1.3,(M_martes:0.6,M_zibellina:1.5):6.5):1.7,M_melampus:3.1):8.6,M_flavigula:15.5):9.0,(M_pennanti:33.8,G_gulo:30.8):3.5);" 169_Strecker_etal_1996_MPE "Strecker, U., C. G. Meyer, C. Sturmbauer, and H. Wilkens. 1996. Genetic divergence and speciation in an extremely young species flock in Mexico formed by the genus Cyprinodon (Cyprinodontidae, Teleostei). Mol. Phylo. Evol. 6:143-149." 100 3 control region mtDNA 349 Neighbor Joining JC none Chordata 13 -3.278981934 0.085678818 . . . "(((((H1:0,H2:33.2,H3:33.2):13.2,H4:27.1):26.5,H5:14.6):18.3,(H6:46.8,H7:11.3):10.2):9.5,(H8:40.1,((H9:18.2,H10:15.3):21.7,(H11:0,H12:70.8,H13:33.8):10.5):7.9):7.0);" 170_Su_etal_1999_MPE "Su, B., Y. -X. Wang, H. Lan, W. Wang, and Y. Zhang. 1999. Phylogenetic study of complete cytochrome b genes in musk deer (genus Moschus) using museum samples. Mol. Phylo. Evol. 12:241-249." 100 2 cyt b mtDNA 1140 Neighbor Joining K2P 14 0.014912281 0.001065163 substitutions/site 0.0115 Chordata 5 0.007462687 0.579858942 0.284367067 0.026954876 3.423572816 "((((fuscus:7.9,leucogaster:6.1):3.8,chrysogaster:11.7):7.5,bijiangensis:24.7):18.4,moschiferus:33.8);" 171_Sumida_etal_2000_MPE "Sumida, M., M. Ogata, and M. Nishioka. 2000. Molecular phylogenetic relationships of pond frogs distributed in the Palearctic region inferred from DNA sequences of mitochondrial 12S ribosomal RNA and cytochrom b genes. Mol. Phylo. Evol. 16:278-285." 100 2 "12S, cyt b" mtDNA 946 Neighbor Joining 21 0.01 0.00047619 substitutions/site 0.0115 Chordata 8 0.443808981 1.435040501 0.270892026 0.012230415 5.639487114 "(((((porosa:0,bre:5.8):35.5,fukien:46.7):18.0,nigro:35.1):36.0,((les:13.2,esc:0):53.8,rid:60.5):60.1):22.2,cates:148.0);" 172_Symula_etal_2003_MPE "Symula, R., R. Schulte, and K. Summers. 2003. Molecular systematics and phylogeography of Amazonian poison frogs of the genus Dendrobates. Mol. Phylo. Evol. 26:452-475." 91 5 "cyt b, COI" mtDNA 722 Maximum Likelihood GTR+I+G none Chordata 12 -0.704122162 1.000545773 . . . "(((((amazonicus:0,ventriculatus1:0):6.9,ventrimaculatus2:11.0):6.6,(variabilis:1.7,ventrimaculatus3:29.0):15.8):9.1,((reticulatus:2.6,species:2.5):13.9,fantasticus:13.2,ventrimaculatus4:64.5):9.0):12.3,(lamasi:3.0,biolat:13.8):34.7,imitator:32.2);" 173_Tang_etal_2003_MPE "Tang, B., K. Zhou, D. Song, G. Yang, and A. Dai. 2003. Molecular systematics of the Asian mitten crabs, genus Eriocheir (Crustacea: Brachyura). Mol. Phylo. Evol. 29:309-316." 100 4 COII mtDNA 529 Maximum Likelihood HKY none Arthropoda 6 0.630139636 1.112923818 . . . "(((((sinensis1:1.6,hepuensis:1.4):14.2,japonica1:16.2):3.2,sinensis2:18.6):3.5,japonica2:22.6):36.0,recta:58.1);" 174_Tougard_etal_2001_MPE "Tougard, C., T. Delefosse, C. Hanni, and C. Montgelard. 2001. Phylogentic relationships of the five extant rhinoceros species (Rinocerotidae, Perissodactyla) based on mitochondrial cytochrome b and 12S rRNA genes. Mol. Phylo. Evol. 19:34-44." 100 3 "12S, cyt b" mtDNA 2146 Maximum Likelihood 19 0.1 0.005263158 substitutions/site 0.0115 Chordata 5 -1.4046875 0.110838027 0.102421873 0.003496747 7.517162622 "(((R_sondaicus:7.7,R_unicornis:5.1):9.5,D_sumatrensis:11.7):2.8,(C_simum:8.0,D_bicornus:13.9):5.3);" 177_vanderKuyl_etal_2002_MPE "van der Kuyl, A. C., D. L. Ph. Ballasina, J. T. Dekker, J. Maas, R. E. Willemsen, and J. Goudsmit. 2002. Phylogenetic relationships among the species of the genus Testudo (Testudines: Testudinidae) inferred from mitochondrial 12S rRNA gene sequences. Mol. Phylo. Evol. 22:174-183." 100 2 12S mtDNA 404 Neighbor Joining K2P 1.075 0.02 0.018604651 substitutions/site 0.0115 Chordata 10 -2.511795542 0.122919067 0.294873995 0.010868834 3.922952443 "(((T_graeca:1.434,(T_kleinmanni:0.486,T_marginata:0.662):1.028):0.328,(T_hermanni:0.661,(T_horsfieldii:1.084,I_elongata:1.954):0.121):0.354):0.319,((G_sulcata:1.305,G_pardalis:2.216):0.093,(G_denticulata:1.817,G_carbonaria:1.516):1.897):0.147);" 178_Vences_etal_2004_MPE "Vences, M., Y. Chiari, L. Raharivololoniaina, and A. Meyer. 2004. High mitochondrial diversity within and among populations of Malagasy poison frogs. Mol. Phylo. Evol. 30:295-307." 88 3 "12S, 16S, cyt b & rhodopsin" mtDNA & nuDNA 2840 Maximum Likelihood GTR+I+G 0.997 0.05 0.050150451 substitutions/site Chordata 14 1.29537814 1.725416038 . . . "(((laevigala:2.083,((species:0.468,expectala:0.482):0.139,(betsileo:0.169,viriolis:0.195):0.211):0.642):0.463,(((crocea:0.051,milorymparium:0.032):0.224,(pulchra:0.232,madagascariensis:0.100):0.166):0.093,aurantiaca:0.238):0.944):0.519,(((nigricans:0.113,baroni:0.072):0.106,baraldmeien:0.176):0.075,cowani:0.220):1.380);" 179_Vink_Paterson_2003_MPE "Vink, C. J., and A. M. Paterson. 2003. Combined molecular and morphological phylogenetic analyses of the New Zealand wolf spider genus Anoteropsis (Araneae: Lycosidae). Mol. Phylo. Evol. 28:576-587." 100 5 COI mtDNA Maximum Likelihood GTR+I+G 0.313 0.01 0.031948882 substitutions/site 0.0115 Arthropoda 20 -3.974130631 0.275742604 0.404562363 0.009092817 3.394472248 "((((((arenvaga:1.422,urquharti:0.061):0.282,(aerescens:0.0,forsteri:0.136):0.904):0.219,(alpina:1.216,montana:0.925):0.371,litoralis:0.805):0.119,canascens:0.663):0.304,((hilaris:1.107,ralphi:0.914,(flavescens:0.26,insularis:0.457):0.192):0.127,(senica:0.525,okatainae:0.584):0.070):0.279,((hallae:0.201,westlandica:0.17):0.348,blesti:0.354):0.28):0.153,((adumbrata:0.934,lacustris:0.977):0.09,cantuaria:0.869):0.307);" 180_Voelker_1999_MPE "Voelker, G. 1999. Molecular evolutionary relationships in the Avian genus Anthus (Pipits: Motacillidae). Mol. Phylo. Evol. 11:84-94." 88 1 cyt b mtDNA 1135 Maximum Likelihood HKY+G none Chordata 39 -4.966680681 0.206801948 . . . "(((sokokensis:1.150,(brachyurus:0.976,caffer:0.978):0.223):0.435,(((((correndera1:0.257,antarcticus:0.347):0.106,correndera2:0.131):0.712,((bogotensis:0.508,hellmayri1:0.533):0.084,hellmayri2:1.449):0.571):0.353,((spraguei:1.320,lutescens:1.185):0.129,furcatus:1.197):0.150):0.278,((((rubescens:0.860,(pratensis:1.050,(spinoletta:0.220,petrosus:1.198):0.116):0.434):0.158,roseatus:1.295):0.107,cervinus:0.723):0.435,(gustavi:2.032,(hodgsoni:0.815,trivialis:0.571):0.526):0.126):0.106):0.300):0.112,((((((((melindae:0.491,similis1:0.444):0.244,(longicaudatus:0.442,vaalensis:0.348):0.126):0.176,(cinnamomeus:1.562,similis2:0.264):0.208):0.232,(leucophrys:0.821,(berthelotii:0.191,campestris:0.749):0.696):0.252):0.075,godlewskii:1.232):0.075,(nyassae:1.355,novaeseelandiae:1.708):0.083):0.049,(richardi:0.254,rufulus:0.657):0.694):0.641,(((lineiventris:0.481,crenatus:1.330):0.592,hoeschi:0.952):0.639,sylvanus:1.785):0.147):0.411);" 181_Wares_201_MPE "Wares, J. P. 2001. Patterns of speciation inferred from mitochondrial DNA in north Ameican Chthamalus (Cirripedia: Balanomorpha: Chthamaloidea). Mol. Phylo. Evol. 18: 104-116." 100 4 COI mtDNA 398 Maximum Likelihood GTR+I+G 1.025 0.05 0.048780488 substitutions/site 0.0115 Arthropoda 9 -2.081559 0.351561594 0.143491909 0.002941418 7.205958406 "((((panamensis:2.967,(((anisoporna:0.665,fissus:0.676):0.495,cortezianus:0.59):0.187,tragilis:1.333):0.618):0.271,(proteus:0.122,mexicanus:0.397):1.14):0.375,dalli:1.473):0.575,angustitergum:0.883);" 182_Weibel_Moore_2002_MPE "Weibel, A. C., and W. S. Moore. 2002. Molecular phylogeny of a cosmopolitan group of woodpeckers (genus Picoides) based on COI and cyt b mitochondrial gene sequences. Molecular Phylogenetics and Evolution 22:65-75." 70 2 "COII, cyt b" mtDNA 1580 Maximum Likelihood GTR+I+G 1.915 0.1 0.052219321 substitutions/site 0.0115 Chordata 25 -2.713320253 0.424756927 0.193056496 0.00162047 9.080692779 "((((((((P_lignarius:0.226,P_mixtus:0.118):0.582,(V_callonotus:0.353,V_nigriceps:0.347):0.145):0.397,(((P_nuttallii:0.168,P_scalaris:0.151):0.618,P_pubescens:0.855):0.162,P_minor:1.034):0.324):0.133,(((P_albolarvatus:0.37,P_stricklandi:0.505):0.146,P_villosus:0.257):0.471,P_borealis:1.048):0.074):0.272,D_fuscescens:1.399,(P_leucotos:0.28,P_major:0.457):0.901):0.197,(((P_canicapillus:0.486,P_maculatus:0.809):0.397,P_kizuki:0.784):0.552,(P_arcticus:1.685,P_tridactylus:1.371):0.407):0.21):0.179,((P_rubiginosus:0.721,C_auratus:0.694):0.37,D_pileatus:1.217):0.684):0.216,(M_carolinus:1.461,S_varius:1.686):0.335);" 186_Whittingham_etal_2002_MPE "Whittingham, L. A., B . Silkas, D. W. Winkler, and F. H. Sheldon. 2002. Phylogeny of the tree swallow genus, Tachycineta (Aves: Hirundinidae), by Bayesian analysis of mitochondrial DNA sequences. Mol. Phylo. Evol. 22:430-441." 100 4 "cyt b, COII, ATPase8" mtDNA 2170 Maximum Likelihood GTR+I+G 1 1 1 substitutions/site 0.0115 Chordata 9 -2.083645776 0.263504508 0.154510557 0.003410502 7.222826087 "((bicolor:0.073,((thalassina:0.079,euchrysea:0.052):0.007,cyaneoviridis:0.063):0.008):0.021,((stolzmanni:0.045,(albilinea:0.030,albiventer:0.026):0.020):0.012,(leucorrhoa:0.021,meyeni:0.013):0.036):0.015);" 188_Yamaguchi_etal_2000_MPE "Yamaguchi, M., M. Miya, M. Okiyama, and M. Nishida. 2000. Molecular phylogeny and larcal morphological diversity of the Lanternfish genus Hygophum (Teleostei: Myctohidae). Mol. Phylo. Evol. 15:103-114." 67 4 16S mtDNA 1172 Maximum Likelihood HKY+I+G 2.546 0.05 0.019638649 substitutions/site 0.0115 Chordata 7 -1.625408836 0.257210648 0.188584999 0.00711286 5.405217942 "((benoiti:1.269,(hygomii:1.748,(taaningi:0.566,macrochir:0.485):1.726):0.396):1.238,(hanseni:2.047,(proximum:2.481,reinhardti:2.509):0.478):0.750);" 189_Ye_etal_2004_MPE "Ye, W., C. -Y. Lee, R. H. Scheffrahn, J. M. Aleong, N. -Y. Su, G. W. Bennett, and M. E. Scharf. 2004. Phylogenetic relationships of neararctic Reticulitermes species (Isoptera: Rhinotermitidae) with particular reference to Reticulitermes arenincola Goellner. Mol. Phylo. Evol. 30:815-822." 100 1 "COII, 12S, 16S" mtDNA 1780 Neighbor Joining HKY+J165+I+G 0.349 0.01 0.028653295 substitutions/site 0.0115 Arthropoda 5 -0.280706522 0.904916667 0.327187501 0.035683887 2.626759674 "(sibialis:1.143,((areolusoni:0.022,finnipes:0.02):0.918,(hageni:0.68,virginicus:0.558):0.305):0.034);" 190_Yokoyama_etal_2000_MPE "Yokoyama, J., M. Suzuki, K. Iwatsuki, and M. Hasebes. 2000. Molecular phylogeny of Coriaria, with special emphasis on the disjunct distribution. Mol. Phylo. Evol. 14:11-19." 100 2 "rbcL, matK" cpDNA 2416 Maximum Likelihood K2P+G 0.667 0.01 0.014992504 substitutions/site Magnoliophyta 12 -0.03813551 0.392337256 . . . "(((terminalis:0.318,myrtifolia:0.224,nepalensis:0.312):0.243,(japonica:0.044,intermedia:0.422):0.568):0.224,(microphylla:0.601,(papuana:0.052,species:0.044,(arborea:0.052,(ruscifolia:0.081,(sarmentosa:0.133,lurida:0.066):0.085):0.208):0.046):0.366):0.209);" 191_Yu_etal_1999_MPE "Yu, H., W. Wang, S. Fang, Y. -P. Zhang, F. -J. Lin, and Z. -C. Geng. 1999. Phylogeny and Evolution of the Drosophila nasuta subgroup based on mitochondrial ND4 and ND4L gene sequences. Mol. Phylo. Evol. 13:556-565. 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Evol. 16:85-95." 54 2 "cyt b, ND4" mtDNA 2523 Neighbor Joining K2P 0.324 0.01 0.030864198 substitutions/site 0.0115 Chordata 18 -3.090391131 0.284823269 0.178321003 0.001987399 8.126058984 "((((((thibetana:1.447,((annectens:0.308,cansus:0.374):0.924,(curzoniae:0.390,nubrica:0.467):0.929):0.089):0.069,daurica:1.740):0.117,thomasi:1.481):0.857,huangensis:2.829):0.144,((hyperborea:1.667,alpina:1.903):0.062,princeps:1.949):0.738):0.074,((forresti:2.393,erythrotis:2.111):0.101,(((koslowi:1.770,ladacensis:2.015):0.345,(roylei:0.636,macrotis:0.555):0.973):0.055,himalayana:2.209):1.340):0.380);" 193_Taylor_etal_1996_MPE "Taylor, D. J., P. D. M. Hebert, and J. K. Colbourne. 1996. Phylogenetics and evolution of the Daphnia longispina group (Crustacea) based on 12S rDNA sequence and allozyme variation. Mol. Phylo. Evol. 5:495-510." 100 3 12S mtDNA 525 Neighbor Joining K2P 0.135 0.01 0.074074074 substitutions/site 0.0115 Arthropoda 14 0.325328863 1.214723697 0.21160836 0.003731508 8.856053735 "(((((longispina:0.676,umbra:0.619):0.151,(((thorata:0,rosea1:0):0.218,((rosea2:0.029,hyalina:0):0.050,rosea3:0.102):0.177):0.191,((galeata:0.051,mendotae:0.066):0.299,cucullata:0.560):0.155):0.226):0.561,longiremis:1.168):0.145,(laevis:0.566,dubia:0.859):0.479):0.108,pulex:1.348);" 194_Cunha_etal_2005_SysBiol "Cunha, R. L., R. Castilho, L. Ruber, and R. Zardoya. 2005. Patterns of cladogenesis in the venomous marine gastropod genus Conus from the Cape Verde Islands. Syst. Biol. 54:634-650." 84 5 "12S, cyt b & lipoprotein" mtDNA & nuDNA 2500 Bayesian GTR+I+G 3.582 30 8.37520938 Million years 1 Mollusca 47 2.507947877 1.783233818 0.215549404 0.001032479 21.25669262 "(((((((((grahami:0.153,decoratus:0.153):0.655,navarroi:0.810):0.193,lugubris:1.000):0.264,raulsilvai:1.257):0.066,((((derrubado:0.058,damottai:0.058):0.262,(diminutus:0.205,boavistensis:0.205):0.118):0.149,(navarroi:0.137,damottai2:0.137):0.327):0.562,((((((((fantasmalis:0.047,messiasi:0.047):0.067,((delanoyi:0.036,luquei:0.036):0.030,maloensis:0.070):0.037):0.019,irregularis:0.138,fuscoflavus:0.138):0.029,teodorae:0.168,iberogermanicus:0.168):0.029,salreiensis:0.192):0.041,crotchii:0.240):0.050,evorai:0.270):0.202,((((felitae:0.127,fontonae:0.127):0.088,(mordeirae:0.132,(cuneolus:0.094,pseudocuneolus:0.094,serranegrae:0.094):0.040,regonae:0.132):0.071):0.070,antoniomonteiroi:0.277):0.047,(longilineus:0.234,miruchae:0.234):0.077):0.169):0.546):0.306):0.097,((borgesi:0.113,josephinae:0.113):0.917,infinitus:1.041):0.388):0.482,(xicoi:0.958,(mercator:0.667,guanche:0.657):0.299):0.945):0.154,ventricosus:2.048):0.484,((((genuanus:0.076,Conus_species1:0.076,venulatus:0.076):0.085,(Conus_species2:0.039,trochulus:0.039):0.138):0.124,ateralbus:0.293):0.302,pulcher:0.587):1.947);" 196_Vogler_etal_2005_SysBiol "Vogler, A. P., A. Cardoso, and T. G. Barraclough. 2005. Exploring rate variation among and within sites in a densly sampled tree: Species level phylogenies of North American tiger beetles (genus Cicindela). Syst. Biol. 54:4-20." 84 2 "cyt b, COI, 16S, ND1" mtDNA 1897 Maximum Likelihood GTR+I+G 0.486 0.026357406 0.054233347 substitutions/site 0.0115 Arthropoda 116 -1.321012705 0.850046995 0.371587259 0.001211203 8.051707969 "((((((((((((((positula:0.062,rufiventris:0.131):0.096,(cazieri:0.072,schauppi:0.117):0.163):0.082,sedecimpunctata:0.24):0.17,((scabrosa:0.042,highlandensis:0.051):0.383,abdominalis:0.469):0.291):0.384,(carthgena:0.154,haemorrhagica:0.1):0.375):0.135,(((((paxensis:0.177,hygrophoba:0.32):0.081,(lotvi:0.223,clarina:0.162):0.094):0.22,ruficapulta:0.462):0.154,nebulder:0.201):0.359,beneshi:0.49):0.135):0.299,clysanterica:0.476):0.388,(((roesiventris:0.347,scrimmeri:0.254):0.478,mathni:0.487):0.297,(pscellata:0.344,fufosenea:0.391):0.448):0.448):0.275,(((((((obsoletanequila:0.043,pesudothalestris:0.039):0.114,(obsoletata:0.222,obsoleta:0.257):0.182):0.141,craven:0.13):0.313,horni:0.531):0.277,(cessa:0.198,nigrilabris:0.212):0.424):0.199,(aternima:0.277,nigrocerulea:0.259):0.553):0.228,(((chrysippe:0.567,guerensis:0.64):0.183,tenuisignata:0.571):0.167,(rugatilis:0.237,punctaulaia:0.394):0.514):0.362):0.276):0.235,((cyanivenra:0.153,seneicolis:0.144):0.97,aurora:1.118):0.433):0.276,(((((((((limgaiis:0.053,decemnotata:0.05):0.004,denverensis:0.029):0.021,(purpurea:0.0,splendida:0.0):0.036):0.525,scultellaria:0.576):0.236,((primeriana:0.119,fulgida:0.152):0.348,parawania:0.349):0.27):0.137,((lengi:0.207,willistoni:0.168):0.454,(traguebarica:0.181,latesignata:0.11):0.618):0.233):0.092,(((longlabris:0.167,nebraskana:0.232):0.116,(secguttata:0.07,patruela:0.061):0.384):0.235,(formosa:0.743,pulchna:0.571):0.163):0.196):0.18,armagossa:0.654):0.33,(((((((((oregona:0.077,depressula:0.027):0.027,belissima:0.03):0.027,limbeta:0.048):0.062,(aurenicola:0.07,colombica:0.037):0.064):0.06,theatina:0.107):0.274,duodecimiguttata:0.442):0.217,rependa:0.665):0.344,maritima:0.506):0.232,hirticolis:0.596):0.387):0.16):0.273,(((((((preateniata:0.018,fulgoris:0.015):0.267,circumpicta:0.395):0.205,(californicarnojavernsis:0.354,californicabrevihamata:0.396):0.31):0.236,(((servera:0.337,striga:0.247):0.461,pamphila:0.687):0.267,logata:0.572):0.174):0.345,gabba:0.926):0.564,(infasciata:0.485,auraria:0.605):0.512):0.28,((((macronema:0.518,leuconce:0.548):0.803,chlorosephalis:0.981):0.604,graphiptera:1.231):0.659,((venusta:0.124,curvata:0.073):0.346,dorsalis:0.415):0.633):0.425):0.321):0.216,(((((schrammeli:0.059,dugeti:0.092):0.278,sinelow:0.184):0.581,schwarzi:0.925):0.136,branchi:0.392):0.507,lemniscata:0.904):0.311):0.348,((((((((((((wapleri:0.105,macra:0.066):0.056,puritana:0.13):0.025,((isoperata:0.016,imaurtha:0.024):0.016,icupraecens:0.099):0.036):0.078,ibianda:0.177):0.106,gratiosa:0.222):0.112,lepida:0.208):0.17,hirliabris:0.359):0.351,invadica:0.49):0.265,(hamata:0.033,marginata:0.102):0.456):0.35,(((hamicola:0.03,icinctpennis:0.0):0.191,inephalota:0.125):0.418,icelenpes:0.456):0.301):0.231,debilis:0.461):0.31,belfragei:0.784):0.303);" 197_Sasaki_etal_2005_SystBiol "Sasaki, T., M. 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"(((bahamaondei:0.286,occidentalis:0.348):1.806,(nenquensis:0.957,affinis:0.683):0.113,(alacalufi:0.616,(manni:0.717,(heuicollensis:0.878,denticulara:0.710):0.062):0.036):0.16):0.149,(((riolimayana:0.401,abiao:0.477):0.446,(spectabile:0.843,(araucaniensis:0.48,(pewenchae:0.588,(laevis:1.164,cholchol:0.905,rostrata:0.921):0.042):0.205):0.11):0.038):0.122,((spinipalma:0.852,(marginata:1.659,(camargoi:1.008,((paulensis:1.247,(perobae:1.971,((parva:0.445,castro:0.945):0.195,((parna:0.667,schmitti:0.574):0.063,(cavernicola:0.396,strinatti:0.496):0.493):0.049):0.263):0.093):0.068,((sp2:0.777,leptodactyla:1.0):0.069,(sp3:1.002,jarai:0.993,spinosa:0.68,odebrechtii:1.2):0.332):0.064):0.048):0.115):0.02):0.03,((((singularis:0.616,platensis:0.689):0.58,((rossiana:0.464,uruguayana:0.664):0.16,platensis:0.675):0.156):0.8,((intercalata:0.872,(prado:1.172,violacea:1.557):0.391):0.287,(humahuaca:1.3,(sp6:1.013,(septentrionalis:1.158,(jujuyana:0.486,sanlorenzo:0.85):0.613):0.174):0.236):0.356):0.055):0.145,((((sp1:0.929,sp5:0.98):0.23,(marginata:0.0,leplchela:0.0):0.629):0.567,(inconspicua:1.316,(serrana:1.215,(franciscana:0.442,ligulata:0.502):0.57):0.134):0.095):0.085,(obstipa:1.214,(sp4:1.047,itacolomiensis:1.901):0.171,(plana:0.725,grisella:0.816,inermis:0.997,longirostri:1.025):0.122):0.25):0.127):0.167):0.303):0.133);" 199_Jordal&Hewitt_2004_SystBiol "Jordal, B. 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Host-symboint stability and fast evolutionary rates in an Ant-bacterium association: Cospeciation of Camponotus species and their endosymboints, Candidatus blochmannia. Syst. Biol. 53:95-110." 100 3 "COI, COII & EF1-alpha" mtDNA & nuDNA Bayesian GTR+I+G 0.29 0.05 0.172413793 substitutions/site Arthropoda 16 -0.952994849 0.648484618 . . . "((((sansabeanus:0.246,vicinus:0.232):0.241,(((laevigaus:0.146,novaboracensis:0.095):0.032,(chromaiodes:0.044,pennsylvanicus:0.054):0.053):0.18,(americanus:0.098,castaneus:0.045):0.233):0.060):0.0789,((sayi:0.307,nearcticus:0.368):0.098,schaefferi:0.445):0.091,ocreatus:0.663):0.165,(((vafer:0.507,festinatus:0.569):0.166,ulcerosus:1.148):0.114,floridanus:0.7):0.331);" 201_Sorenson_etal_2004_SysBiol "Sorenson, M. D., C. N. Balakrishnan, and R. B. Payne. 2004. Clade-limited colonization in brood parasitic finches (Vidua spp.). Syst. 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Biol. 52: 794-819." 100 8&9 "12S, 16S" mtDNA 2430 Bayesian GTR+I+G 0.356 0.05 0.140449438 substitutions/site 0.0115 Chordata 50 -4.07215974 0.317776743 0.132448989 0.000365474 16.50719279 "((((((kardasian:0.651,microdiscus:0.866):0.185,(gyldenstolpei:0.337,laticeps:0.287):0.105):0.373,kuhlii2:0.377):0.385,kuhlii1:0.639):0.391,(kuhlii3:0.346,asperatus:0.168):0.552):0.243,(leporinus:0.697,((fincki:0.194,(palavanensis:0.352,parvus:0.099):0.094):0.652,((((((blythii1:0.3,((blythii2:0.247,macrodon:0.235):0.143,(ingeri:0.139,malesiana:0.155):0.193):0.175):0.503,paramacrodon:0.734):0.095,blythii3:0.262):0.188,ibanorum:0.281):0.345,(grunniens:0.25,((EC:0.058,WC:0.36):0.044,(SE:0.086,(EC:0.065,Togian:0.082):0.021):0.053):0.181):0.438):0.292,((((leytensis_boh:0.118,leytensis_sam:0.117):0.026,leytensis_sib:0.120):0.102,leytensis_min:0.265):0.608,((cf_acanthi:0.384,acanthi:0.649):0.272,((((((((magnus:0.594,magnuscf:0.567):0.076,((macrocephalus:0.449,visayanus:0.539):0.123,woodworthi:0.571):0.099):0.123,(modestus1:0.359,modestus2:0.551):0.418):0.1,(((spV1:0.131,spV2:0.441):0.362,heinrichi:0.495):0.212,spT:0.764):0.098):0.069,sp1:0.661):0.221,spG2:1.047):0.095,(microtympanum1:0.519,microtympanum2:0.533):0.173):0.135,((spD:0.362,sp2:0.725):0.244,arathooni:0.441):0.137):0.172):0.245):0.421):0.185):0.291):0.34);" 204_Nepokroeff_etal_2003_SysBiol "Nepokroeff, M., K. J. Sytsma, W. L. Wagner, and E. A. Zimmer. 2003. Reconstructing ancestral patterns of colonization and dispersal in the Hawaiian understory tree genus Psychotria (Rubiaceae):a comparison of parsimony and likelihood approaches. Syst. Biol. 52:820-838." 100 3 ITS nuDNA 1171 Maximum Likelihood K80+G 0.26 0.05 0.192307692 substitutions/site 0.00305 Magnoliophyta 12 -0.167856296 0.717695041 0.037244254 0.000138713 49.85468545 "(((((marianiana:0.064,hawaiiensis:0.321):0.194,wawae:0.143):0.146,((((hawaiiensis:0.135,mauiensis:0.0):0.096,(fauriei:0.121,hathewayi:0.137):0.08):0.025,kaduana:0.076):0.035,greenwelliae:0.133):0.379):0.222,(grandiflora:0.204,hobdyi:0.43):0.569):0.021,hexandra:0.77);" 205_Yang&Yoder_2003_SystBiol "Yang, Z., and A. D. Yoder. 2003. Comparison of likelihood and Bayesian methods for estimating divergence times using multiple gene loci and calibration points, with application to a radiation of cute-looking mouse lemur species. Syst. Biol. 52:705-716." 100 1 "COII, cyt b" mtDNA Bayesian JC 4.412 90 20.39891206 Million years 1 Chordata 9 -1.450050951 0.223259251 0.167638278 0.004014656 7.916902766 "((ravelobensis:0.302,(sambiranensis:0.178,rufus2:0.162,tavaratra:0.149,(rufus1:0.092,berthae:0.096,myoxinus:0.096):0.074):0.133):0.082,(griseorufus:0.286,murinus:0.291):0.106);" 207_Jordan_etal_2003_SystBiol "Jordan, S., C. Simon, and D. Polhemus. 2003. Molecular systematics and adaptive radiation of Hawaii's endemic damselfly genus Megalagrion (Odonata: Coenagrionidae). Syst. Biol. 52:89-109." 100 5 COII mtDNA 1287 Maximum Likelihood GTR+I+G 43.2 0.1 0.002314815 substitutions/site 0.0115 Arthropoda 22 0.291763323 0.634531027 0.212371489 0.002255082 12.61751089 "((((((hawaiiense:16.3,(((paludicola:6.2,mauka:8.4):10.6,((vagabundum:0,eudytum2:1.3):2.0,((eudytum1:2.2,adytum:1.6):2.5,species_nov:1.3):2.0):6.3):4.5,(nesioles:6.0,oahuense:8.5):7.8):0.7):6.4,koelense:30.0):1.9,((blackburni:15.2,oceanicum:9.2):8.9,heterogamlas:12.3):11.3):2.0,kaualense:14.2):23.8,(pacificum:3.0,xanthomolas:7.4):56.9):9.7,((nigrohamatum:26.6,orobustes:29.2):35.2,((leptodemas:11.8,calliphya:6.2):27.0,oresitrophum:18.8):13.5):9.6);" 208_Hormiga_etal_2002_SystBiol "Hormiga, G., M. Arnedo, and R. G. Gillespie. 2003. Speciation on a conveyor belt: Sequential colonization of the Hawaiian islands by Orsonwelles spiders( Araneae, Linyphiidae). Syst. Biol. 52:70-88." 92 7 "COII, 16S & 28S, 18S, ITS, EF1-alpha" mtDNA & nuDNA Maximum Likelihood TVM+I+G 109.3 6 0.054894785 Million years 1 Arthropoda 12 -1.867238488 0.259534783 0.365356331 0.013348525 4.133234218 "((calx:46.8,((iudicium:13.1,bellum:13.1):5.0,ventus:18.1):28.3):28.5,(malus:66.5,(arcanus:47.4,((ambersonorum:27.5,polites:27.5):12.5,((falstaffius:27.4,graphicus:27.4):7.5,(othello:26.3,macbeth:26.3):8.6):5.4):7.4):19.0):9.0);" 210_Packert_etal_2005_BJLS "Packert, M., J. Martens, S. Eck, A. A. Nazarenko, O. P. Valchuk, B. Petri, and M. Veith. 2005. The great tit (Parus major)-a misclassified ring species. Biol. J. Linn. Soc. 83:153-174." 100 3 cyt b mtDNA 580 Bayesian TrN+I+G 2.137 0.1 0.046794572 substitutions/site 0.0115 Chordata 5 0.239246013 0.839475462 0.35633881 0.042325782 2.852434345 "(monticolus:0.918,((bok:0.124,maj:0.075):0.250,(cin:0.266,min:0.191):0.10):0.145);" 211_VonRintelen&Glaubrecht_2005_BJLS "Von Rintelen, T., and M. Glaubrecht. 2005. Anatomy of an adaptive radiation: a unique reproductive strategy in the endemic freshwater gastropod Tylomelania (Cerithioidea: Pachychilidae) on Sulawesi, Indonesia and its biogeographical implications. Biol. J. Linn. Soc. 85:513-542." 100 14 16S mtDNA 890 Bayesian 9.5 0.011235955 0.001182732 substitutions/site 0.0115 Mollusca 15 0.163003383 1.478005979 0.698355038 0.037515366 2.597939402 "((((carbo:3.0,toradjarum:4.0):9.8,(neritiformis:0,porcellanica:3.0,centaurus:0):13.2):5.6,kuli:24.3):10.2,((gemmifera:4.1,patriarchalis:5.0,zeamais:6.6):6.5,(towutensis:3.2,towutica:0):9.1):10.8,(kruimeli:14.0,(insulaesacrae:2.2,sarasinorum:3.2):9.1):17.3,perfecta:16.8);" 212_Warren_etal_2005_BJLS "Warren, B. H., E. Bermingham, R. P. Prys-Jones, and C. Thebaud. 2005. Tracking island colonization history and phenotypic shifts in Indian ocean bulbuls (Hysipetes: Pycnonotidae). Biol. J. Linn. Soc. 85:271-287." 100 3 ND3 mtDNA Bayesian GTR+G none Chordata 7 -1.386369474 0.225119282 . . . "(((barbonicus:3.1,(madagascariensis1:10.5,olivaceus:4.6):3.1):2.0,((crassirotris:5.5,madagascariensis2:11.9):1.7,parvirostris:8.5):3.1):10.0,philippinus:18.5);" 213_Amer&Kumazawa_2005_BJLS "Amer, S. A. M., and Y. Kumazawa. 2005. Mitochondrial DNA sequences of the Afro-Arabian spiny-tailed lizards (genus Uromastyx; family Agamidae): phylogenetic analyses and evolution of gene arrangements. Biol. J. Linn. Soc. 85:247-260." 69 5 ND2 mtDNA 1503 Neighbor Joining HKY+J178+I+G 31 0.1 0.003225806 substitutions/site 0.0115 Chordata 9 -1.51066933 0.30751971 0.110861855 0.001755764 12.36938817 "(hardwickii:45.2,((macfadyeni:24.9,(geyri:12.9,(acanthinura:7.8,dispar:9.9):3.3):11.5):4.1,(aegyptia:25.4,(benti:21.2,(ocellata:17.7,ornata:15.1):4.1):5.0):2.2):14.8);" 214_Tucker_etal_2005_BJLS "Tucker, P. K., S. A. Sandstedt, and B. L. Lundrigan. 2005. Phylogenetic relationships in the subgenus Mus (genus Mus, family Muridae, subfamily Murinae): examining gene trees and species trees. Biol. J. Linn. Soc. 84:653-662." 100 2 "cyt b, 12S & B2m, Zp3, Tcp1,Sry,Smcx, Smcy" mtDNA & nuDNA 8170 Maximum Likelihood TrN+I+G 6.8 0.01 0.001470588 substitutions/site Chordata 7 -1.285273149 0.158281053 . . . "((M_m:8.8,((macedonius:4.7,spicilegus:5.2):3.5,spretus:11.2):1.6):14.3,((cervicolor:13.0,cookii:10.0):3.1,caroli:17.5):3.0);" 215_Lavrenchenko_etal_2004_BJLS "Lavrenchenko, L. A., E. Verheyen, S. G. Potapove, V. S. Lebedev, N. SH. Bulatova, V. M. Aniskin, W. N. Verheyen, and A. P. Ryskov. 2004. Divergent and reticulate processes in evolution of Ethiopian Lophuromys flavopunctatus species complex: evidence from mitochondrial and nuclear DNA differentiation patterns. Biol. J. Linn. Soc. 83:301-316." 100 3 "16S, cyt b" mtDNA 874 Neighbor Joining TrN+I+G 77.3 0.1 0.001293661 substitutions/site 0.0115 Chordata 13 -1.907911693 0.319794683 0.428895082 0.016722817 3.634232398 "((L_sikapusi:19.8,L_ansorgei:28.5):6.5,(((L_brunneus:14.0,((L_brevicaudus:23.0,((L_melanonyx:10.7,(Menagesha:6.2,North_II:7.0):2.2):2.5,Chercher:13.2,L_sikapusi:9.7):4.3):1.1,(L_flavopunctatus:3.2,L_brunneus2:4.4):11.0):1.4):2.0,North_I:21.1):2.5,L_chrysopus:30.0):7.8);" 216_Chapple&Keough_2003_BJLS "Chapple, D. G., and J. S. Keogh. 2004. Parallel adaptive radiations in arid and temperate Australia: molecular phylogeography and systematics of the Egernia whitii, (Lacertilia: Scincidae) species group. Biol. J. Linn. Soc. 83:157-173." 91 2 "ND4, 16S & b-Fibrinogenintro" mtDNA & nuDNA 1844 Maximum Likelihood GTR+I+G 15.2 0.05 0.003289474 substitutions/site Chordata 15 -3.540486335 0.148906713 . . . "((((((margaretae:6.3,whiteii:6.4):15.9,(montana:16.1,guthega:15.2):2.8):0.6,personata:19.0):2.0,(margaretae:23.1,modesta:23.8):3.6):2.6,(((inornata:12.1,multiscutata:15.5):0.9,(kintorei:6.0,striata:9.8):5.2):4.3,pulchra:21.0):3.0):4.8,((saxatilis:16.8,spp:26.7):1.0,major:16.3):8.1);" 219_Gaubert_etal_2004_BJLS "Gaubert, P., C. A. Fernandes, M. W. Bruford, and G. Veron. 2004. Genets (Carnivora, Viverridae) in Africa: an evolutionary synthesis based on cytochrome b sequences and morphological characters. Biol. J. Linn. Soc. 81:589-610." 100 1 cyt b mtDNA 1140 Maximum Likelihood GTR_G 61.7 0.1 0.001620746 substitutions/site 0.0115 Chordata 15 -2.182308875 0.395558668 0.36354174 0.010166354 4.561307198 "(thierryi:35.9,(victoriae:6.1,((servalina:10.9,cristata:6.5):13.2,((piscivora:18.8,johnstoni:25.8):6.3,(genetta2:33.5,((angolensis:8.5,genetta1:17.0):6.2,((pardina:7.0,(poensis:5.0,(bourloni:2.8,schoutedeni:11.7):1.7):7.4):3.0,(maculata:4.0,tigrina:3.4):7.6):6.7):6.5):7.1):4.0):7.7):7.3);" 221_ParraOlea_etal_2004_BJLS "Parra-Olea, G., M. Garcia-Paris, and D. B. Wake. 2004. Molecular diversification of salamanders of the tropical American genus Bolitoglossa (Caudata: Plethodontidae) and its evolutionary and biogeographical implications. Biol. J. Linn. Soc. 81:325-346." 100 4 "cyt b, 16S" mtDNA 1196 Maximum Likelihood GTR+I+G 4.5 0.05 0.011111111 substitutions/site 0.0115 Chordata 55 -4.995217274 0.303262045 0.131360648 0.000325578 14.8839446 "(((dofleini:14.0,alvaradoi:9.5):6.0,((((((alberchi:4.5,((mexicana:3.0,(mombachoensis:0.9,striatula:1.4):2.9):1.4,yucatana:4.1):1.2):0.7,odonnelli:4.0):2.8,(flaviventris:9.0,platydactyla:5.0):1.7):4.5,((accidentalis:10.0,rufescens:16.4):12.2,hartwegi:8.3):2.5):4.0,(((((adspersa:3.2,species1:3.5):0.4,(sima:6.1,biseriata:5.4):4.4):0.5,((medemi:11.6,palmata:4.2,(peruviana1:9.1,paraensis:9.7):1.2):0.4,(altamazonica:4.6,peruviana2:4.6):2.0):1.0):4.5,((species2:7.3,schizodactyla:7.0):0.5,colonnea:10.2):1.7):3.7,((cerroensis:5.5,((marmorea:2.8,epimela:8.6):0.4,minutula:5.8):1.3):3.4,(((subpalmata:2.7,species4:2.5):0.4,gracilis:4.0):0.5,pesrubra:3.5):5.8):1.7):7.6):1.8,((((((morio:1.4,flavimembris:2.5):6.6,(carri:5.8,(conanti:5.2,(diaphora:5.6,dunni:5.3):0.5):1.1):0.7):1.1,((celaque:1.5,synoria:2.2):1.8,species3:5.0):2.0):0.8,(decora:6.8,(longissima:7.5,porrasorum:5.5):0.9):0.5):1.7,(franklini:3.0,lincolni:3.2):5.3):2.6,(engelhardti:5.5,rostrata:6.0):4.9):1.6):1.7):1.2,(((hermosa:2.9,rileta:3.9):5.4,zapoteca:5.1):1.9,(macrinii:2.7,oaxacensis:2.3):3.7):3.6);" 222_Steppan_etal_2003_BJLS "Steppan, S. J., C. Zawadzki, and L. R. Heaney. 2003. Molecular phylogeny of the endemic Philippine rodent Apomys (Muridae) and the dynamics of diversification in an oceanic archipelago. Biol. J. Linn. Soc. 80:699-715." 77 4 cyt b mtDNA 1144 Maximum Likelihood TrN+G 59.3 6 0.101180438 Million years 1 Chordata 10 -1.825873475 0.325721289 0.268842798 0.009034556 4.79342325 "(((((AC:21.5,B:21.5):3.7,musculus:24.8):5.0,microdon:30.3):6.1,(((hylocoetes:2.0,insignis:2.0):15.9,F:17.7):10.0,D:27.9):8.4):11.2,(datae:38.8,gracilirostris:38.8):8.5);" 223_Suzuki_etal_2003_BJLS "Suzuki, H., J. J. Sato, K. Tsuchiya, J. Luo, Y. -P. Zhang, Y. -X. Wang, and X. -L. Jiang. 2003. Molecular phylogeny of wood mice (Apodemus, Muridae) in east Asia. Biol. J. Linn. Soc. 80:469-481." 100 4 IRBP nuDNA 1152 Maximum Likelihood K2P 92 0.04 0.000434783 substitutions/site Chordata 14 -0.732158988 0.983881119 . . . "(((agrarius:4.7,chevrieri:4.7):42.8,((draco:8.4,semolus:8.4):8.1,latronum:16.5):31.0,peninsulae:47.5,speciosus:47.5):9.5,argerateus:57.0,guricha:57.0,(alpicola:13.5,flavicollis:13.5,sylvanicus:13.5,(uraiensis:2.2,wardi:2.2):11.3):43.5);" 224_Tsigenopoulos_etal_2003_BJLS "Tsigenopoulos, C. S., J. D. Durand, E. Unlu, and P. Berrebi. 2003. Rapid radiation of the Mediterranean Luciobarbus species (Cyprinidae) after the Messinian salinity crisis of the Mediterranean sea, inferred from mitochondrial phylogentic analysis. Biol. J. Linn. Soc., 80:207-222." 100 2 cyt b mtDNA 1140 Maximum Likelihood TrN+I+G 56 8 0.142857143 Million years 1 Chordata 33 -4.006790356 0.302336143 0.333640836 0.003590845 5.511755958 "((((((((Barbus_species3:5.6,callensis2:5.6):11.9,(Barbus_species4:13.0,callensis1:13.0):4.6):1.3,((moulouyensis:16.6,pallaryi:16.6):1.2,nasus:17.8):0.9):0.3,biscarensis:19.2,(((magniatlantis:11.5,labiosa:11.5):2.2,Barbus_species2:13.7):3.4,massaensis:17.0):2.2):3.2,lepineyi:22.5):7.9,(((rajanorum:6.8,xanthopierus:6.8):7.1,capito2:13.9,longiceps:13.9):4.0,(capito1:13.9,brachycephalus:13.9):4.0):12.5):5.8,((((bocagei:4.8,comizo:4.8):12.3,(setivimensis:15.6,sclateri:15.6):1.5):5.4,((guiraonis:5.5,microcephalus:5.5):3.7,graellsii:9.3):13.4):12.5,(((angorae:14.6,capocta:14.6):13.5,trutta:28.2):3.1,subquincunciatus:31.3):3.9):1.1,(graecus:28.0,albanicus:28.0):7.8):2.3,mursa:38.8);" 228_Garcia_etal_2002_BJLS "Garcia, G., F. Alvarez-Valin, and N. Gomez. 2002. Mitochondrial genes: signal and noise in the phylogenetic reconstruction of the annuall killfish genus Cynolebias (Cyprinodontiformes, Ricuildae). Biol. J. Linn. Soc. 76:49-59." 56 4 "cyt b, 12S, 16S" mtDNA 1825 Neighbor Joining K2P 1.3 0.005874 0.004518462 substitutions/site 0.0115 Chordata 12 -4.301417996 0.036481025 0.1956369 0.00382738 4.866760113 "((((((adioffi:12.0,viarius:9.1):2.3,(beilottil:9.0,nioni:9.0):1.3):1.5,gymnovenris:15.2,(wolterstorffi:11.5,cheradophilus:6.7):1.3):3.7,nigripinnis:17.6):2.4,(cyaneus1:5.5,(duraznensis:7.9,affinis:6.7):3.7):3.6):6.1,cyaneus2:3.0);" 229_Ota_etal_2002_BJLS "Ota, H., M. Honda, S. -L. Chen, T. Hikida, S. Panha, H. -S. Oh, and M. Matsui. 2002. Phylogenetic relationships, taxonomy, character evolution and biogeography of the lacertid lizards of the genus Takydromus (Reptilia: Squamata): a molecular perspective. Biol. J. Linn. Soc. 76:493-509." 76 3 "12S, 16S" mtDNA 829 Maximum Likelihood 37.2 0.1 0.002688172 substitutions/site 0.0115 Chordata 13 -1.949324085 0.309771068 0.163395836 0.002427109 9.212285091 "((kuehnei:25.6,sexlineatus:38.6):9.6,(tachydromoides:32.5,((smaragdinus:22.1,(dorsalis:18.2,sauteri:15.9):6.0):3.0,(amurensis:17.7,((hsuehshanensis:9.5,(wolteri:11.0,formosanus:8.2):2.5):4.5,(toyami:10.5,(stejnegeri:6.3,septentrionalis:6.8):3.4):10.3):10.0):6.7):4.0):5.1);" 230_Remigio_etal_2001_BJLS "Remigio, E. A., P. D. N. Hebert and A. Savage. 2001. Phylogenetic relationships and remarkable radiation in Parartemia (Crustacea: Anostraca), the endemic brine shrimp of Australia: evidence from mitochondrial DNA sequence. Biol. J. Linn. Soc. 74:59-71." 100 4 16S mtDNA 350 Neighbor Joining K2P 9.3 0.5 0.053763441 substitutions/site 0.0115 Arthropoda 13 -2.093977601 0.36875815 0.048714286 0.000215735 30.31011384 "(((((longicaudata:0.9,POP3:1.7):0.5,POP1:1.1):2.8,(cylindifera:2.3,(POP5:3.6,zietziana:3.2):2.3):1.6):0.7,(extracta:3.4,((contracta:0,serventyi:5.9):2.9,(POP2:1.2,informis:0):2.3,POP4:2.1):1.4):0.7):2.5,minuta:5.2);" 231_Kimball_etal_2001_BJLS "Kimball, R. T., E. L. Braun, J. D. Ligon, V. Lucchini, and E. Randi. 2001. A molecular phylogeny of the peacock-pheasants (Galliformes: Polyplectron spp.) indicates loss and reduction of ornimental traits and display behaviours. Biol. J. Linn. Soc. 73:187-198." 100 3 cyt b mtDNA 1143 Maximum Likelihood HKY+G 18.1 0.1 0.005524862 substitutions/site 0.0115 Chordata 6 -0.337575394 0.548457803 0.209722917 0.010995926 5.149531701 "(((((P_bicalcaratum:1.9,P_chalcurum:1.7):1.7,P_inopinatum:3.0):1.5,P_germaini:3.8):3.6,P_malacense:10.0):3.0,P_emphanum:9.5);" 232_Goodacre&Wade_2001_BJLS "Goodacre, S. L., and C. M. Wade. 2001. Patterns of genetic variation in Pacific island land snails: the disribution of cytochrome b lineages among Society Island Partula. Biol. J. Linn. Soc. 73:131-138." 100 2 cyt b mtDNA 682 Maximum Likelihood GTR+I+G 18.8 0.1 0.005319149 substitutions/site 0.0115 Mollusca 20 -1.458690302 0.529019242 0.119488008 0.000793188 16.84252641 "(((((tristis:27.0,affinis1:18.6):3.7,(filosa:10.6,otaheitana1:14.1):6.3):1.0,(((((mirabilis:6.4,(affinis2:4.5,otaheitana2:4.5):8.5):4.5,suturalis2:3.2):5.0,taeniata2:1.1):1.0,suturalis1:2.6):7.0,nodosa:12.2):10.6,suturalis3:24.1):1.0,((((mooreana:4.2,taeniata1:5.1):2.0,taeniata3:5.0,tohiveana:5.0):13.1,clara:17.9):11.6,(rosea:22.7,varia:19.6):6.4):1.0):6.3,hebe:39.4);" 234_Mascheretti&Mirol_2000_BJLS "Mascheretti, S., and P. M. Mirol. 2000. Phylogenetics of the speciose and chromosomally variable rodent genus Ctenomys (Ctenomyidae, Octodontoidea), based on mitochondrial cytochrome b sequences. Biol. J. Linn. Soc. 70: 361-376." 62 2 cyt b mtDNA 382 Neighbor Joining K2P 38 0.1 0.002631579 substitutions/site 0.0115 Chordata 27 -2.608324573 0.524701641 0.424074338 0.007193562 4.577582805 "((((((((((pilarensis:1.5,occultus:2.1):1.1,argentinus:1.7):0.7,latro:4.5):8.1,juris:3.3):3.4,leucodon:24.0):0.9,((roigi:3.0,dorbignyi:2.4):6.9,opimus:10.7):1.7):1.0,(((((boliviensis2:3.0,goodfellowi:3.6):6.9,(boliviensis1:5.0,nattereri:4.3):9.0):1.5,steinbachi:16.0):2.9,tucumanus:9.0):0.7,haigi:9.5):1.0,(((bergi:0,bonettoi:2.4):2.7,(mendocinus:7.6,azarae:7.0):0.7):2.5,(pundti:5.0,talarum:1.6):5.7):1.8):1.0,scagliai:13.1):2.5,tuconax:25.7):2.3,((conoveri:12.8,lewisi:9.0):1.0,frater:12.5):4.6);" 235_Johnson_etal_2005_AnEntSocAm "Johnson, D. G., B. C. Carstens, W. S. Sheppard, and R. S. Zach. 2005. Phylogeny of leafhopper subgenus Errhomus (Erronus) (Hemiptera: Cicadellidae) based on mitochondrial DNA sequences. Ann. Entomol. Soc. Am. 98:165-172." 57 3 ND1 mtDNA 600 Maximum Likelihood GTR+I+G 4.5 0.05 0.011111111 substitutions/site 0.0115 Arthropoda 13 2.807756312 0.275289276 0.084851873 0.000654531 47.20787996 "((((montana:4.2,camensis:3.5):0.5,((bracatus:2.5,(naomi:3.7,solus:3.6):0.7):0.8,(affinis:3.3,((pallidus:0.6,variabillis:2.3):3.5,serratus:2.0):0.3):1.1):0.5):3.7,rivalis:3.6):40.0,(calvus:0,(ochoco:0.8,similis:1.2):1.5):50.5);" 236_Spicer&Bell_2002_AnnEntSocAm "Spicer, G. S., and C. D. Bell. 2002. Molecular phylogeny of the Drosophila virilis species group (Diptera:Drosophilidae) inferred from Mitochondrial 12S and 16S ribosomal RNA genes. Systematics 95:156-161." 100 4 "12S, 16S" mtDNA 1311 Maximum Likelihood GTR+I+G 2.92 20 6.849315068 Million years 1 Arthropoda 14 -0.156235724 1.024274011 0.160073093 0.002135283 10.87128995 "(((((avericava:0.036,novanexicene:0.036):0.109,texene:0.134):0.676,haumei:0.812):0.117,virilis:0.919):0.67,(kinerkoi:1.399,(exaene:0.984,(littoralis:0.086,canadensis:0.086):0.903):0.424):0.186,(borealis_E:0.907,(((borealis_W:0.114,bacicola:0.114):0.059,monatana:0.165):0.431,flavasulasa:0.596):0.317):0.665);" 237_Kruse&Sperling_2002_AnEntSocAm "Kruse, J. J., F. A. H. Sperling. 2002. Phylogeny of neararctic species of the Xylosteana group of Archips Hubner (Lepidoptera: Tortricidae) based on combined analysis of morphological and mitochondrial DNA data sets. Ann. Entomol. Soc. Am. 95:288-301." 100 4 COI mtDNA 816 Maximum Likelihood HKY+I+G 0.191 0.005 0.02617801 substitutions/site 0.0115 Arthropoda 18 -2.595447386 0.33898424 0.302637774 0.005724351 4.929717644 "((((((tarsina:1.242,fuscacapreana:0.866):0.088,((negundlana:0.834,semiferana:0.555):0.697,(greisca:0.884,magnoliana:1.231):0.125):0.242):0.116,(((argyrospila:0.615,goyerana:0.389):0.630,urgriplagana:1.289):0.527,georgiana:1.873):0.246):0.161,((infumatara:0.746,(ferridana:0.708,cerasivarana:0.769):0.188):1.017,rileyana:1.671):0.544):0.152,((packardiensis:0.127,alberta:0.232):0.371,striana:0.394):1.571):0.251,purpurana:1.928);" 238.1_Church&Taylor_2005_AJB "Church, S. A., and D. R. Taylor. 2005. Speciation and hybridization among Houstonia (Rubiaceae) species: the influence of polyploidy on reticulate evolution. Amer. J. Bot. 92:1372-1380." 68 2 "trnS-G, trnL" cpDNA 973 Maximum Likelihood GTR+I+G 0.565 0.005 0.008849558 substitutions/site Magnoliophyta 7 -3.064956143 0.025758325 . . . "((((serpyllifolia:2.244,caeralea:0.677):0.475,(pusilla:1.57,micrantha:0.947):1.317):0.456,(rosea:1.709,procumbens:1.673):1.186):0.141,serpyllifolia:0.913);" 238.3_Church&Taylor_2005_AJB "Church, S. A., and D. R. Taylor. 2005. Speciation and hybridization among Houstonia (Rubiaceae) species: the influence of polyploidy on reticulate evolution. Amer. J. Bot. 92:1372-1380." 68 4 "trnS-G, trnL" cpDNA 973 Maximum Likelihood GTR+I+G 0.358 0.005 0.01396648 substitutions/site Magnoliophyta 7 -1.350583621 0.332478896 . . . "(((rubra:1.987,wrightii:0.0):1.142,humifusa:2.495):0.145,((acerosa:1.634,palmeri:0.354):0.425,(nigricans:0.246,butterwickiae:0.324):0.314):0.189);" 239_Chung_2005_AJB "Chung, K. -F., C. I. Peng, S. R. Downie, K. Spalik, and B. A. Schaal. 2005. Molecular systematics of the trans-Pacific alpine genus Oreomyrrhis (Apiaceae):phylogenetic addinities and biogeographic implications. Amer. J. Bot. 92:2054-2071." 52 4 ITS nuDNA 607 Maximum Likelihood GTR+G 0.138 0.008237232 0.059690089 substitutions/site 0.00305 Magnoliophyta 34 -0.744077784 0.76883665 0.340779299 0.003629079 8.244014011 "(((((andicola:0.037,(argentea:0.03,brevipes:0.069,ciliata:0.0,eropoda:0.034):0.027,(bomeensis:0.059,nanjuensis:0.051):0.045,azoreallacae:0.041,(colensoi:0.047,ramosa:0.080):0.05,eropoda:0.042,gunnii:0.047,lijnearis:0.042,papuana:0.086):0.029,(procumbens:0.047,tainturieri:0.033):0.193):0.083,temulum:0.537):0.174,((((((aromaticum:0.053,atlanticum:0.053):0.064,azoricum:0.117):0.054,bulbosum:0.0):0.068,((astrantiae:0.076,macrospermum:0.088):0.064,macropodum:0.219):0.037,aureum:0.144):0.052,(byzantium:0.025,libanoticum:0.03):0.208,(crinitum:0.113,khorossanicum:0.393):0.021,meyeri:0.089):0.401,nodosun:0.074):0.048):0.048,(elegans:0.017,magellense:0.134,villarsii:0.154):0.216);" 243_Cieslak_etal_2005_AJB "Cieslak, T., J. S. Polepalli, A. White, K. Muller, T. Borsch, W. Barthlott, J. Steiger, A. Marchant, and L. Legendre. 2005. Phylogenetic analysis of Pinguicula (Lentibulariaceae): chloroplast DNA sequences and morphology support several geographically distinct radiations. Amer. J. Bot. 92:1723-1736." 51 3 "matK, trnK" cpDNA 2560 Bayesian GTR+I+G 0.275 0.01 0.036363636 substitutions/site Magnoliophyta 40 0.962688408 1.353478917 . . . "(((((((((((sp:0.0,rectifolia:0.0):0.016,emarginata:0.055):0.023,sp:0.083):0.025,((moranensis:0.0,laureana:0.014):0.062,medusina:0.186):0.034):0.025,(moctezumae:0.052,accuminata:0.059):0.076):0.054,((agnata:0.024,gigantea:0.056):0.042,sharpii:0.371):0.035):0.053,(esseriana:0.057,ehlersiae:0.081):0.09):0.053,((gracilis:0.0,rotundiflora:0.041):0.14,filifolia:0.37):0.031):0.122,alpina:0.284):0.074,((ramosa:0.193,villosa:0.33):0.032,variegata:0.419):0.087):0.021,((frandiflora:0.024,fontiqueriana:0.04,bulgaris:0.019,macroceras:0.023,mundi:0.02,nevadensis:0.042,vulgaris:0.028,fiorii:0.02,longifolia:0.02,corsica:0.032,vallisneriifolia:0.019):0.08,((leproceras:0.03,congifolia:0.065):0.087,poldinii:0.108):0.056):0.111,(((ionantha:0.066,primulifolia:0.102):0.023,lutea:0.071):0.417,(crystallina:0.555,lustanica:0.122):0.177):0.114);" 248_Kay_etal_2005_AJB "Kay, K. M., P. A. Reeves, R. G. Olmstead, and D. W. Schemske. 2005. Rapid speciation and the evolution of hummingbird pollination in neotropical Costus subgenus Costus (Costaceae): evidence from nrDNA ITS and ETS sequences. Amer. J. Bot. 92:1899-1910." 75 supplied by author "ITS, ETS" nuDNA 1309 Bayesian K80+G 1 1 1 substitutions/site 0.00305 Magnoliophyta 38 -5.571546393 0.198704506 0.02867473 2.284E-05 59.98810893 "((mont:0.145743,(com:0.09262300,(osa:0.07189800,lim:0.092579):0.01014100):0.02963400):0.08298700,(((((malo:0.09288500,(amaz:0.07143700,((aspl:0.10284600,(arab:0.07197000,(clav:0.01001600,guan:0.02011300):0.01026200):0.093523):0.02047600,(varz:0.09391500,(eryt:0.07134200,lon:0.05315300):0.03143300):0.032242):0.04810700):0.01062300):0.02013600,((((((alle:0.05323200,vill:0.07978300):0.03961500,(guan:0.08263100,(leuc:0.05055600,(varz:0.08260200,(ery:0.07914300,spir:0.070512):0.01183300):0.01967600):0.02106900):0.03149400):0.02308300,(brac:0.07193500,lasi:0.081893):0.04781100):0.01477000,(wils:0.061174,laev:0.040035):0.143825):0.02004300,barb:0.07112100):0.01087200,((zin:0.18957500,char:0.12587300):0.03981500,(pro:0.07167400,((pulv:0.065335,(spic:0.01005500,scab:0.021038):0.09236600):0.01973900,(wood:0.040557,(wils:0.060343,pul_OsaBE:0.060252):0.009882):0.01117900):0.06854500):0.01201900):0.02000200):0.01039500):0.05442200,vin:0.13690400):0.02006000,sten:0.16646300):0.01073700,(dirz:0.08153900,pic:0.06020900):0.01605400):0.01041800);" 249_Lee_etal_2005_AJB "Lee, C., S. -C. Kim, K. Lundy, and A. Santos-Guerra. 2005. Chloroplast DNA phylogeny of the woody Sonchus alliance (Asteraceae: Sonchinae) in the Macaronesian islands. Amer. J. Bot. 92:2072-2085." 100 4 "matK, trnK & ITS" cpDNA & nuDNA 4728 Maximum Likelihood GTR+I 0.334 0.0005 0.001497006 substitutions/site Magnoliophyta 26 -2.223480579 0.520027738 . . . "((pinnatifidus:0.161,(brachylobus:0.281,(wildpretii:0.134,arborea:0.287):0.265):0.153):0.139,((tuberifer:1.107,fauces_orci:0.827):0.135,(pinnata:0.146,canariensis:0.274,(microcarpa:0.0,capillaris:0.0):0.291,heterophylla:0.687,(gonzalezpadronii:0.155,ortunoi:0.41,radicatus:0.0,tectifolius:0.148):0.264):0.4,((ustulatus:0.101,(pinnatus:0.154,fruticosus:0.0):0.671):0.139,(congestus:0.273,(acaulis:0.556,(palmensis:0.425,canariensis:0.144):0.28,(gandogeri:0.29,daltonii:0.15,hierrensis:0.154,bornmuelleri:0.0):0.414):0.135):0.273):0.268):0.144);" 250_Lledeo_etal_2005_AJB "Lledo, M. D., M. B. Crespo, M. F. Fay, and M. W. Chase. 2005. Molecular phylogenetics of Limonium and related genera (Plumbaginaceae): biogeographical and systematic implications. Amer. J. Bot. 92:1189-1198." 100 2 "rbcL, trnL, trnl-F" cpDNA 2473 Maximum Likelihood TVM+I+G 3.904 15 3.842213115 Million years 1 Magnoliophyta 45 -5.778672696 0.159319574 0.175348876 0.000715052 12.05294562 "((((macrophyllum:1.393,arborescens:1.393):0.188,(svenlenii:1.254,fruticaris:1.254):0.331):0.282,((((spectabile:0.816,moretii:0.816):0.484,lobatum:1.306):0.246,beaurnieranum:1.553):0.042,sinuatum:1.604):0.261):1.28,((((((((A_peregrinum:0.771,A_purpuratum:0.771):0.323,(narbonense:0.517,vulgare:0.517):0.577):0.185,camosum:1.290):0.222,globufiferum:1.51):0.556,(pectinatum:1.612,(stocksii:0.961,(somatorum:0.788,axillare:0.788):0.173):0.645):0.457):0.159,((tenetium:0.8,(sinense:0.755,tetragonum:0.755):0.044):0.938,bellioifolium:1.745):0.483):0.137,((((echioides:1.206,(thiniense:0.455,perplexum:0.455):0.764):0.197,rigualii:1.427):0.348,((((((((duloni:0.765,densissimum:0.765):0.216,santapolense:0.995):0.103,densissimum:1.098):0.194,furfuraceum:1.301):0.109,binerosum:1.419):0.047,(parvixacteatum:0.901,biflorum:0.901):0.566):0.043,carthagienese:1.508):0.179,((((cossoniarium:0.454,delicatulum:0.454):0.372,girarmarium:0.819):0.372,estevei:1.209):0.269,mansanetiarium:1.473):0.201):0.084):0.383,((insigne:1.428,caesium:1.428):0.21,tuberculatum:1.645):0.544):0.167):0.222,dendroides:2.598):0.548);" 251_Mansion&Zeltner_2004_AJB "Mansion, G., and L. Zeltner. 2004. Phylogenetic relationships within the new world endemic Zelthnera (Gentianaceae-Chironiinae) inferred from molecular and karyological data. Amer. J. Bot. 91:2069-2086." 92 29 "trnL, trnL-F & ITS" cpDNA & nuDNA 1271 Maximum Likelihood GTR+G 77.9 18 0.231065469 Million years 1 Magnoliophyta 25 -0.913512315 0.818768807 0.284966758 0.003530698 7.239148763 "(Z_abramsii:31.5,(((((Z_namophila:1.0,Z_malenbergii2:1.0):1.0,Z_nevadensis:2.0):5.5,Z_trichantha:7.6):19.0,((Z_venusta:4.0,Z_mahlenbergii:4.0):21.0,(Z_exaltata:3.4,Z_undet:3.4):21.6):1.4):3.1,(Z_multicaulis:23.8,(Z_arizonica:10.6,(Z_maryanna:9.4,(Z_glandulifera:8.4,(Z_beyrichii:7.6,(Z_breviflora:6.0,(Z_calycosa:2.1,Z_texensis:2.1):4.0):1.6):0.4):0.8):1.0):12.8):5.5,((Z_undet_bis:19.6,(Z_martinii:10.9,(Z_madrensis:6.7,Z_setacea:6.7):4.2):8.5):3.5,(Z_quitensis:18.9,(Z_stricta:7.3,(Z_pusilla:5.2,Z_wigginrii:5.2):2.1):11.6):4.3):6.1):1.9);" 253_McKown_etal_2005_AJB "McKown, A. D., J. -M. Moncalvo, and N. G. Dengler. 2005. Phylogeny of Flaveria (Asteraceae) and inference of C4 photosynthesis evolution. Amer. J. Bot. 92:1911-1928." 91 2 ITS nuDNA 708 Bayesian GTR+I+G 2.1 0.001412429 0.000672585 substitutions/site 0.00305 Magnoliophyta 22 -0.907656724 0.926157988 0.224676263 0.002523971 7.907502366 "((((((floridana:3.2,linearis2:4.8):5.8,(oppositifolia:1.8,pubescens:0):2.8,brownii:4.3,linearis1:14.7,chloraefolia:9.3):21.1,anomala:49.6):5.8,((((trinervia:0,australasica:2.2):7.1,((kochiana:6.2,vaginata:3.3):4.5,bidentis:9.5):16.2):6.1,(campestris:12.4,palmeri:6.4):13.5):13.4,ramosissima:20.0):17.7):3.0,(pringlei2:6.2,angustifolia:3.5):30.0,(robusta:28.9,sonorensis:31.6):2.9):7.3,(pringlei:25.2,cronquistii:19.7):3.1);" 257_Schnabel_etal_2003_AJB "Schnabel, A., P. E. McDonel, and J. F. Wendel. 2003. Phylogenetic relationships in Gleditsia (Leguminosae) based on Its sequences. Amer. J. Bot. 90:310-320." 85 3 ITS nuDNA 707 Maximum Likelihood HKY+G 1 1 1 substitutions/site 0.00305 Magnoliophyta 11 0.042098457 0.952952542 0.571875 0.036337891 2.909836066 "((amorphoides:0.01,(rolfei:0.001,sinensis:0.001):0.002):0.001,((microphylla:0.006,(fera:0.002,australis:0.003):0.002):0.003,((delavayi:0.001,japonica:0.001,capsica:0.001):0.006,(aquatica:0.001,triacanthos:0.0):0.001):0.004):0.002);" 258_Scheuttpelz&Hoot_2004_AJB "Schuettpelz, E., and S. B. Hoot. 2004. Phylogeny and biogeography of Caltha (Ranunculaceae) based on chloroplast and nuclear DNA sequences. Amer. J. Bot. 91:247-253." 100 2 "atpB-rbcL, trnL-F & ITS" cpDNA & nuDNA 2166 Maximum Likelihood GTR+I+G 14.7 0.01 0.000680272 substitutions/site Magnoliophyta 10 -0.736775593 0.499937964 . . . "(natans:28.8,((scaposa:13.8,palustris:18.9):11.0,(leptosepala:14.0,(sagittata:26.0,((appendiculata:11.5,dionaeifolia:11.1):3.5,(obtusa:1.5,introloga:2.9,novaezelandiae:6.2):6.3):5.9):5.4):19.1):9.4);" 261_Bell&Patterson_2000_AJB "Bell, C. D., and R. W. Patterson. 2000. Molecular phylogeny and biogeography of Linanthus (Polemoniaceae). Amer. J. Bot. 87:1857-1870." 93 5 ITS nuDNA 568 Maximum Likelihood GTR+G 42.5 10 0.235294118 Million years 1 Magnoliophyta 48 -2.449791068 0.491563336 0.271339347 0.001600544 11.23706344 "((((((((((((bicolor:2.0,jepsonii:2.0):11.6,parviflorus:13.6):1.3,androsaceus:14.7):1.9,((((pachyphyllus:1.4,melingii:1.4):2.5,floribundus:3.9):0.3,nuttallii:4.2):3.7,laxus:7.6):8.9):2.0,acicularis:18.7):1.1,(septentrionalis:12.3,harknessi:12.3):7.0):0.6,(((filipes:10.5,pusillus:10.5):2.7,((balanderi:0.0,rattanii:0.0):1.0,ambiguas:1.7):11.1):0.4,pygmaeus:13.3):6.9):2.0,(((montanus:11.0,ciliatus:11.0):7.5,((breviculus:7.9,aureus:7.7):8.0,jamaensis:16.2):2.6):2.0,nudatus:20.7):1.6):1.4,((grandiflorus:2.8,lemmonii:2.8):1.4,liniflorus:4.0):19.0):19.2):3.9,(P_gracilis:11.0,(P_stansburyi:5.5,(P_hoodii:1.5,P_diffusa:1.5):4.0):5.4):32.0):3.9,(((((((((jonesi:11.5,(dichotomus:9.2,bigelovii:9.2):2.2):1.1,pareyae:12.0):0.4,(arenicola:10.7,killipii:10.7):1.9):1.5,pungens:13.8):0.6,(caespitosum:7.4,watsonii:7.4):6.6):3.9,((bellus:14.0,orcuttii:14.0):3.3,demissus:17.3):0.8):6.7,((dianthiflorius:14.8,uncialis:14.8):7.6,concinnus:22.4):2.5):3.8,G_maculata:28.2):2.8,G_filiformis:31.0):15.8);" 264_Davis_etal_2002_SystBot "Davis, C. C., P. E. Fritsch, J. Li, and M. J. Donoghue. 2002. Phylogeny and biogeography of Cercis (Fabaceae): Evidence from nuclear ribosomal ITS and chloroplast ndhF sequence data. Syst. Bot. 27: 289-302." 100 4 ndhF & ITS cpDNA & nuDNA 620 Maximum Likelihood GTR+I+G 1 1 1 substitutions/site Magnoliophyta 6 -0.379296278 0.490783531 . . . "((((canadensis:0.00226142,siliquastrum:0.002261420):0.0000000000000002658,occidentalis:0.002261430):0.005087850,(chinensis:0.006323174,gigantea:0.006323):0.001026105):0.003797961,chingii:0.011147241);" 265_Downie_etal_2004_SystBot "Downie, S. R., F-J. Sun, D. S. Katz-Downie, and G. J. Colletti. 2004. A Phylogenetic Study of Perideridia (Apiaceae) based on nuclear ribosomal DNA ITS sequences. Syst. Bot. 29: 373-751." 100 2 ITS nuDNA 603 Maximum Likelihood TrN+G 3 0.005 0.001666667 substitutions/site 0.00305 Magnoliophyta 15 -3.026767316 0.217661365 0.103807114 0.000828917 13.49620318 "((((((((bolanderi:12.0,((bacigalupii:5.0,involucrata:8.8):3.9,erythrorhiza:9.4):1.0):0.3,lemmonii1:9.4):5.5,(parishii:7.5,lemmonii2:4.8):5.5):2.8,(californica:12.7,pringlei:17.4):1.2):4.7,kelloggii:20.9):3.2,howellii:18.0):3.2,(gairdneri:16.3,(leptocarpa:8.5,oregana:11.4):6.5):2.3):0.7,americana:27.2);" 266_Feng_etal_2005_SystBot "Feng, Y., S.-H. Oh, and P. S. Manos. 2005. Phylogeny and historical biogeography of the genus Platanus as inferred from nuclear and chloroplast DNA. Syst. Bot. 30:786-799." 86 4 "trnT-L & ITS, LEAFY" cpDNA & nuDNA 3125 Maximum Likelihood TrN+I+G 5.6 0.001 0.000178571 substitutions/site Magnoliophyta 4 0.225986859 0.103238815 . . . "((mexicana:16.5,occidentalis:16.7):40.9,(orientalis:30.9,racemosa:27.9):55.7);" 267_Freeman_etal_2003_SystBot "Freeman, C. E., J. S. Harrison, J. P. Janovec, and R. Scogin. 2003. Inferred phylogeny in Keckiella (Scrophulariaceae) based on noncoding choloplast and nuclear ribosomal DNA sequences. Syst. Bot. 28:782-790." 100 3 "trnL, trnL-F & ITS" cpDNA & nuDNA 1261 Maximum Likelihood TIM+G 13.8 0.005 0.000362319 substitutions/site Magnoliophyta 7 -2.444385086 0.10977026 . . . "(((((K_corymbosa:17.9,K_lemmonii:20.7):2.7,K_ternata:22.7):3.7,K_breviflora:13.0):9.0,(K_cordifolia:8.9,K_antirrhinoides:11.1):5.1):13.0,K_rothrockii:18.1);" 269_IckertBond&Wojciewchowski_2004_SystBot "Ickert-Bond, S. M., and M. F. Wojciechowski. 2004. Phylogenetic relationships in Ephedra (Gnetales): Evidence from nuclear and chloroplast DNA sequence data. Syst. Bot. 29:834-849. " 100 2 ITS nuDNA 1158 Maximum Likelihood HKY85+G 1.9 0.001 0.000526316 substitutions/site 0.00305 Magnoliophyta 40 2.387927587 1.50496558 0.6655737 0.011657588 6.692845825 "(((sinica:3.8,intermedia:1.9,(fedtschenkoae:3.8,regeliana:0.0):1.5):6.0,((strobilacea:0.0,(sarcocarpa:0.0,transitoria:3.9):1.7):11.3,distachya:7.6):1.7):24.7,(((pachyclada:0.0,somalensis:1.8):3.4,(monosperma:7.6,saxatilis:7.7):5.8):21.9,(pedunculata:21.0,(((americana:7.6,repsetris:6.0):1.6,(chilensis:4.5,(tweediana:2.8,triandra:3.2):5.5):4.9,(frustillata:0.0,breana:4.0,americana:0.0,(gracilis:3.7,rupestris:0.0,ochreata:0.0,(multiflora:3.8,boelkei:0.0):1.6):3.7):1.7):10.2,(compacta:12.5,(viridis:7.0,((californica:7.5,trifurca:11.5):15.5,((antisyphilitica:0.0,coryi:0.0):3.6,(aspera:0.0,torryeana:0.0,antisyphilitica:0.0,nevadensisi:0.0,cultleri:0.0,fasciculata:5.9,(torreyana:0,funerea:0):7.4):1.6):12.2):5.5):13.3):1.8):6.6):13.8):8.0);" 270.1_Kita&Kato_2004_SystBot "Kita, Y., and M. Kato. 2004. Molecular phylogeny of Cladopus and Hydrobryun (Podostemaceae, Podostemoideae) with implications for their biogeography in East Asia. Syst. Bot. 29:921-932." 100 4 matK & ITS cpDNA & nuDNA 2090 Maximum Likelihood 10.8 0.005 0.000462963 substitutions/site Magnoliophyta 10 -2.16632102 0.324123009 . . . "((sp1:19.1,bifoliatum:19.1):22.5,((((micrantherum:28.6,sp2:28.6):4.4,((koribanum:22.2,puncticulatum:22.2):1.6,(floribundum:1.8,japonicum:1.8):22.0):9.0):2.8,griffithi:36.0):2.6,sp3:38.5):3.2);" 270.2_Kita&Kato_2004_SystBot "Kita, Y., and M. Kato. 2004. Molecular phylogeny of Cladopus and Hydrobryun (Podostemaceae, Podostemoideae) with implications for their biogeography in East Asia. Syst. Bot. 29:921-932." 77 4 matK & ITS cpDNA & nuDNA 2090 Maximum Likelihood 0.428 0.005 0.011682243 substitutions/site Magnoliophyta 8 2.118925644 1.376675626 . . . "((((austrsinensis:0.180):0.073,austrosinensis:0.236):0.362,(japonicus:0.0,chinensis:0.0,dolanus:0.0,austrosatsumensis:0.0):0.601):0.612,(taiensis:0.404,nymanii:0.404):0.819);" 271_Liu_etal_2002_AJB "Liu, Q., C. L. Brubaker, A. G. Green, D. R. Marshall, P. J. Sharp, and S. P. Singh. 2001. Evolution of the FAD2-1 fatty acid desaturase 5' UTR intron and the molecular systematics of Gossypium (Malvaceae). Amer. J. Bot. 88:92-102." 100 1 FAD2-1 nuDNA 1133 Bayesian TrN+G 18.5 0.01 0.000540541 substitutions/site Magnoliophyta 35 -2.87378611 0.269622051 . . . "((acmalense:11.0,stockeii:17.3):12.5,(((herbaceum:3.0,arboreum:8.6):3.6,darwinii:5.4,barbadense:3.9,hirsulum:5.9,tomentosum:3.9,mustelinum:2.5):11.3,((australa:5.0,nelsonii:8.0):6.9,((((((londonderreinae:7.2,speciesnovum:8.0,cunninghamii:7.1):2.3,nobile:7.9):0.3,marchantii:5.7):1.0,(populifolium:5.8,costolatum:6.3):3.1):1.0,pulchellum:7.0):4.1,(((enthyle:5.5,exiguum:4.3):1.4,pilosum:8.6):1.7,rotundifolum:3.8):2.6):5.4,(robinsonii:15.0,sturtianum:12.2):0.8):5.6):2.7,(((((raymondii:10.5,((tomatosum:4.2,hirsutum:0.9,(barbadense:1.0,darwinii:2.8):1.1):1.9,mustelinum:6.4):8.8):3.2,hrotrachianum:13.9):3.6,turnori:13.7):2.0,trilobum:15.2):0.4,gossyoioidea:11.5):17.5);" 272_Lohwasser_etal_2004_SystBot "Lohwasser, U., A. Granda, and F. R. Blattner. 2004. Phylogenetic analysis of Microseris (Asterceae), including a newly discovered andean population from Peru. Syst. Bot. 29:774-780." 100 2 ITS nuDNA 649 Neighbor Joining HKY+I+G none Magnoliophyta 16 0.532242249 0.295056142 . . . "(((pygmaea:7.9,biglovii:16.9,campsetris:6.3,elegans:10.4):49.8,((decipiens:12.1,(acuminata:3.5,douglasii:21.8):11.2):4.2,heterocarpa:1.3):36.4):4.0,((((laciniata:0.0,borealis:0.0,sylvatica:15.3):1.6,(howellii:4.9,nutans:5.5):6.0):4.2,paludosa:15.0):27.9,(lanceolata:0.0,scapigera:0.0):19.7):18.0);" 274_Roalson_etal_2003_SystBot "Roalson, E. H., L. E. Skog, and E. A. Zimmer. 2003. Phylogenetic relationships and the diversification of floral form in Achimenes (Gesneriaceae). Syst. Bot. 28:593-608." 74 3 trnL-F & ITS cpDNA & nuDNA 1556 Maximum Likelihood TrN+I+G 4.5 0.005 0.001111111 substitutions/site Magnoliophyta 19 -0.369696836 0.804679245 . . . "((((admirabilis:9.3,(cetoana:10.7,longiflora:10.9):3.6):4.9,erecta:5.5):19.6,(((((candida:15.7,grandiflora:17.9):5.5,(antirhina:0.0,pedunculata:2.9):12.5):6.3,((((dileis:4.5,mexicana:5.1):1.4,((flava:5.6,occidentalis:9.9):1.3,hintoniana:3.2):1.3):3.2,patens:4.5):1.3,woodii:5.9):1.5):2.3,majaritensis:23.9):11.7,fubriata:43.6):19.5):2.8,(misera:19.5,glabrata:58.7):2.8);" 275_Schraschkin&Dolye_2005_SystBot "Scharaschkin, T., and J. A. Doyle. 2005. Phylogeny and historical biogeography of Anaxagorea (Annonaceae) using morphology and non-coding choloplast sequence data. Syst. Bot. 30:712-735." 96 5 "atpB-rbcL, psbA-trnH, trnL-F" cpDNA 2251 Bayesian GTR+G 9 0.01 0.001111111 substitutions/site Magnoliophyta 24 -3.70841432 0.377770866 . . . "(inundata:3.5,(angustifolia:10.0,rheophytica:11.3):4.3,(dolichocarpa:1.3,floribunda:45.0,guatemalensis:13.0,macrantha:34.0,pachypetala:1.9,(brevidedicellata:5.9,gigantophylla:18.1):3.2,(panamensis:3.0,(alleni:1.8,crassipetala:1.6):1.7):2.1,(borneensis:3.9,(brachycarpa:3.0,brevipes:1.9):0.9):0.7,(luzonensis:21.2,(javanica:9.0,sylvatica:9.8):1.8):1.5,(phaeocarpa:3.8,prinoides:11.2,(acuminata:0.9,manausensis:0.7,petiolata:5.4):1.8):1.1):9.0);" 276_Simpson_etal_2004_SystBot "Simpson, B. B., A. Weeks, D. M. Helfgott, and L. L. Larkin. 2004. Species relationships in Krameria (Krameriaceae) based on ITS sequences and morphology: Implications for character utility and biogeography. Syst. Bot. 29:97-108." 94 2 inset ITS nuDNA 822 Maximum Likelihood GTR+I+G 1.7 0.006426735 0.003780432 substitutions/site 0.00305 Magnoliophyta 17 3.189251611 1.810379452 0.153066138 0.00156195 26.06664674 "(((((argentea:0.8,(grandiflora:0,spartioides:0):0.9):0.8,ixine:1.8):1.6,tomentosa:3.5):5.1,((((erecta:0,lanceolata:0):0.8,pauciflora:0.5,revoluta:0):0.6,secundiflora:0.7):0.8,ramosissima:1.6):7.3):10.8,((cistoidea:1.0,lappacea:1.0):3.0,(cytisoides:7.0,(grayi:3.0,(paucifolia:0.5,sonorae:1.1):1.1):5.5):3.2):15.2);" 279_Gaubert&Veron_2003_PRSL "Gaubert, P. and G. Vernon. 2003. Exhaustive sample set among Viverridae reveals the sister-group of felids: the linsangs as a case of extreme morphological convergence within Feliformia. Proc. Roy. Soc. Lond., B 270:2523-2530." 100 3 cyt b & TR-I-I mtDNA & nuDNA 1862 Maximum Likelihood GTR+G 30.3 0.1 0.00330033 substitutions/site Chordata 22 -2.225682252 0.442422759 . . . "(N_binotata:25.8,((P_pardicolor:30.0,(Felis:15.4,Panthera:11.3):19.0):3.9,((C_crocuta:33.0,(C_ferox:25.3,H_ichneumon:22.2):6.2):4.9,((C_owstoni:28.7,(P_larvata:8.7,P_hermaphroditus:12.7):14.2):5.4,((C_civetta:14.1,(V_indica:15.1,(V_tangalunga:7.5,(V_zibetha:5.2,V_megaspila:3.7):1.8):8.3):2.6):7.9,(P_richardsonii:9.4,(G_thierryi:11.6,(G_servalina:5.8,((G_piscivora:4.7,G_johnstoni:6.8):1.5,(G_maculata:5.8,G_genetta:4.7):2.4):0.4):2.6):5.3):9.8):0.9):5.0):1.5):4.5);" 280_Cheviron_etal_2005_Auk "Cheviron, Z. A., A. P. Capparella, and F. Vuilleumier. 2005. Molecular phylogenetic relationships among the Geositta miners (Furnariidae) and biogeographic implications for avian speciation in Fuego-Patagonia. Auk 122:158-174." 100 1 "cyt b, ND2, ND3" mtDNA 868 Maximum Likelihood GTR+I+G 10.8 0.05 0.00462963 substitutions/site 0.0115 Chordata 11 -2.349803683 0.051355926 0.102503431 0.001167439 14.65504344 "(((cunicularia:9.2,tenuirostris:14.3):8.5,peruviana:21.5):15.7,(((antarctica:13.9,(isabellina:10.8,saxicolina:11.9):3.0):1.5,maritima:16.3):10.7,((poecilopterus:19.5,crassirostris:18.9):0.6,(punensis:16.0,rufipennis:9.6):3.2):0.7):13.6);" 281_Gill_etal_2005_Auk "Gill, F. B., B. Slikas, and F. H. Sheldon. 2005. Phylogeny of titmice (Paridae): II. Species relationships based on sequences of the mitochondrial cytochrome-B gene. Auk 122:121-143." 78 1 cyt b mtDNA 1068 Bayesian GTR+I+G 17.8 0.066 0.003707865 substitutions/site 0.0115 Chordata 35 -5.309285115 0.204350981 0.208774372 0.00132081 7.212641267 "((((((((((atricapillus:5.8,gambeli:12.0):3.9,sclateri:12.8):0.9,((rufescens:6.3,hudsonicus:4.2):1.1,cinctus:4.5):2.5):1.3,carolinensis:9.0):2.5,((palustris:10.8,montanus:12.1):0.8,davidi:11.3):1.0):2.0,superciliosus:21.1):0.7,varius:16.1):0.7,lugubris:12.4):4.5,((cristatus:7.5,dichrous:11.5):4.7,(wollweberi:10.2,(inornatus:15.1,bicolor:15.1):10.2):4.6):2.7,(((ater:3.6,melanolophus:2.0):9.1,(rubidiventris:16.5,rufonuchalis:16.6):5.0):2.1,(elegans:5.0,amabilis:4.2):6.8):3.7):1.8,(((major:7.4,monticolus:9.4):8.0,((holsti:15.5,(spilonotus:8.6,xanthogenys:7.2):7.0):4.0,afer:17.0):1.2):1.9,(((aliventris:10.5,niger:7.8):5.7,funereus:21.5):2.3,(rufiventris:22.1,fasciiventer:22.1):1.3):1.5):1.5);" 282_Given_etal_2005_Auk "Given, A. D., J. A. Mills, and A. J. Baker. 2005. Molecular evidence for recent radiation in southern hemisphere masked gulls. Auk 122: 268-279." 90 3 "ATPase6, ATPase8, ND2, ND5" mtDNA 3661 Maximum Likelihood GTR+I+G 106.2 3 0.028248588 Million years 1 Chordata 9 0.321827553 1.056295569 0.905040162 0.117013956 1.853107373 "(((((hartlaubii:2.9,cirrocephalus:2.9):11.0,ridibundus:13.9):5.1,(novaehollandiae:8.8,bulleri:8.8):10.2,serranus:19.0):0.6,maculipennis:19.6):46.0,(philadelphia:59.4,genei:59.4):6.2);" 285_Johnson_etal_2006_Science "Johnson, W. E., E. Eizirik, J. Pecon-Slattery, W. J. Murphy, A. Antunes. E. Teeling, and S. J. O'Brien. 2006.The late Miocene radiation of modern Felidae: a genetic assessment. Science 311:73-77." 100 1 lots nuDNA 18853 Maximum Likelihood GTR+I+G 10.2 0.005 0.000490196 substitutions/site Chordata 38 -2.372714967 0.306271421 . . . "((((((((((((F_catus:2.0,F_silvestris:1.5):1.0,(F_libyca:3.0,F_bieti:1.8):0.8):2.2,F_margarita:6.5):1.3,F_nigripes:4.5):1.0,F_chaus:6.0):5.8,(O_manul:12.9,(P_rubiginosus:6.1,((P_bengalensis:3.5,P_viverrinus:6.1):1.1,P_planiceps:5.0):3.0):2.5):0.6):1.2,((P_concolor:7.2,P_yagouaroundi:6.2):1.0,A_jurbatus:9.8):3.1):1.2,(((L_pardinus:2.1,L_lynx:1.7):0.6,L_canadensis:2.0):2.4,L_rufus:6.8):7.5):1.7,((L_pardalis:4.2,L_weidii:3.1):2.0,((L_jacobita:3.4,L_colocolo:1.4):2.8,((L_geoffroyi:2.0,L_guigna:2.0):0.7,L_tigrinus:2.0):2.7):1.2):11.5):1.4,((C_caracal:3.6,C_aurata:4.2):7.4,C_serval:11.1):5.5):1.9,((P_badia:5.3,P_temminckii:7.0):2.0,P_marmorata:10.1):6.2):3.1,((((P_leo:2.0,P_onca:4.5):0.9,P_pardus:4.1):1.3,(P_tigris:3.6,P_uncia:6.0):1.5):4.2,N_nebulosa:9.6):8.3);" 286_Lovette&Bermingham_1999_PRSL "Lovette, I. J., and E. Bermingham. 1999. Explosive speciation in the new world Dendrorica Warblers. Proc. Roy. Soc. Lond., B 266:1639-1636." 89 2 "cyt b, ND2, ATPase 6,8, COI" mtDNA 3639 Maximum Likelihood GTR+G 110.8 0.05 0.000451264 substitutions/site 0.0115 Chordata 26 -4.182586149 0.267322157 0.313600663 0.004097724 4.492287902 "(((((((((D_adelaidae:56.3,(D_discolor:53.2,((D_graciae:14.0,D_nigrescens:14.0):29.6,((D_occidentalis:9.9,D_townsendi:9.9):7.0,D_virens:16.7):26.7):10.3):3.3):33.9,((D_coronata:77.2,(D_dominica:72.3,(D_pinus:51.8,D_pityophila:51.8):20.5):5.0):3.9,D_palmarum:81.0):9.1):4.2,(D_caerulescens:93.2,(((D_castanea:71.0,D_fuscus:71.0):8.4,(D_pensylvanica:47.7,(D_petechia:45.0,D_striata:45.0):3.0):31.5):11.7,D_magnolia:90.9):2.4):1.2):3.8,D_cerulea:97.5):1.6,D_tigrina:99.3):4.1,Setophaga:103.2):9.0,D_plumbea:111.7):1.8,(D_angelae:105.9,Catharopeza:105.9):7.6):1.0,D_pharetra:114.3);" 287_Mooers_etal_1999_AmNat "Mooers, A. O., S. M. Vamosi, and D. Schluter. 1999. Using phylogenies to test macroevolutionary hypotheses of trait evolution in cranes (Gruinae). Amer. Natur. 154:249-259." 100 2 cyt B mtDNA Maximum Likelihood 16.4 0.01 0.000609756 substitutions/site 0.0115 Chordata 13 -2.565802998 0.189190999 0.378576703 0.01302912 3.541887026 "((G_japonensis:47.9,(G_americana:27.2,(G_grus:23.4,(G_monachus:13.9,G_nigricollis:13.9):9.5):3.8):20.7):18.8,((G_leucogeranus:50.8,(G_antigone:34.5,(G_vipio:25.5,G_rubicunda:25.5):9.0):16.3):11.7,(G_canadensis:55.4,(B_carunculatus:47.7,(A_paradisea:25.4,A_virgo:25.4):22.3):7.7):7.5):4.2);" 288_Price_etal_2000_AmNat "Price, T., I. J. Lovette, E. Bermingham, H. L. Gibbs, and A. D. Richman. 2000. Imprint on history on communities of North American and Asian Warblers. Amer. Natur. 156:354-367." 100 1 cyt b mtDNA 1000 Neighbor Joining HKY+G 17 0.01 0.000588235 substitutions/site 0.0115 Chordata 8 -3.274095846 0.008406865 0.520639408 0.045177566 1.71355413 "((P_megrirostris:24.8,(P_trochioides:21.7,P_occipitalis:21.7):3.1):8.7,(P_tytleri:27.6,P_alfinis:27.6):6.0,((P_pulcher:24.7,P_chloronctus:24.7):1.3,P_hunai:26.0):7.4);" 289_Roukonen_etal_2000_JEB "Ruolonen, M., L. Kvist, and J. Lumme. 2000. Close relatedness between mitochondrial DNA from seven Anser good species. J. Evol. Biol. 13:532-540." 100 2 control region mtDNA 1180 Maximum Likelihood K2P 1.182 0.0107 0.009052453 substitutions/site 0.0115 Chordata 7 0.09126557 0.055471817 0.667914773 0.089222029 2.135886927 "(((pink_footed:0.676,(tundra_bean:0.543,lesser_white_fronted:0.443):0.55):0.952,(Greenland_whitefront:0.554,European_whitefront:0.628):0.896):0.952,(western_greylag:0.394,eastern_greylag:0.587):2.335);" 291_Thulin_etal_2004_SystBot "Thulin, M., M. Lavin, R. Pasquet, and A. Delgado-Salinas. 2004. Phylogeny and biogeography of Wajira (Leguminosae): a monophyletic segregate of Vigna centered in the horn of Africa region. Syst. Botany 29:903-920." 100 2 trnK & ITS cpDNA & nuDNA 3505 Bayesian GTR+I+G 38.8 10 0.257731959 Million years 1 Magnoliophyta 39 -3.515816657 0.284614434 0.211771648 0.001212087 10.77784938 "((W_danissana:21.1,(W_albescens:17.5,((W_virescens:12.2,W_praecox:12.2):3.0,W_grahamiana:15.2):2.7):3.4):20.9,(((S_stenocarpa:3.8,S_angustifolia:3.8):32.0,((M_daltonii:4.5,M_ellipticum:4.5):23.0,(D_trilobus:20.2,N_holosericea:20.2):7.3):8.3):4.2,((D_lignosus:5.2,L_purpureus:5.2):22.5,(S_kilimandscharicum:18.6,V_pseudolablab:18.6):9.1,((P_venenosum:22.7,((V_luteola:16.0,(V_trichocarpa:6.6,(V_longifolia:4.0,V_lasiocarpa:4.0):2.6):9.4):1.0,(V_monophylla:15.9,(V_friesiorum:13.2,V_unguiculata:13.2,(V_mungo:5.0,V_umbellata:5.0):8.2):2.7):1.1):5.7):3.2,(P_vulgaris:20.3,(R_strobilophora:12.6,O_volubilis:12.6):7.7,((V_ekmaniana:15.5,(V_peduncularis:13.5,V_latidenticulata:13.5):2.0):2.2,(((D_paraguariensis:12.0,S_umbellata:12.0):2.1,(M_uleanus:12.1,M_atropurpureum:12.1):2.0):2.2,((V_linearis:7.4,V_spectabilis:7.4):6.0,(V_gentryi:2.1,V_adenantha:2.1):11.3):2.7):1.7):2.6):5.6):2.0):12.3):1.6);" 292_vonRintelen_etal_2004_PRSLB "Von Rintelen, T., A. B. Wilson, A. Meyer, and M. Glaubrecht. 2004. Escalation and trophic specialization drive adaptive radiation of freshwater gastropods in ancient lakes on Sulawesi, Indonesia. Proc. Roy. Soc. Lond., B 271:2541-2549." 100 3 COI & 16S mtDNA 1480 Neighbor Joining HKY+I+G 0.18 0.003378378 0.018768769 substitutions/site 0.0115 Mollusca 93 2.004116001 1.384104121 1.876072573 0.038677454 2.529491604 "(((((((((a:0.081,b:0.05):0.019,(c:0.0,d:0.0):0.038):0.015,e:0.111,f:0.07):0.337,(g:0.047,h:0.11):0.4):0.329,(i:0.245,j:0.22):0.418):0.082,((((((((k:0.07,l:0.065):0.048,m:0.174,n:0.206):0.037,(o:0.111,p:0.081):0.024):0.044,(((q:0.094,r:0.141):0.067,s:0.127):0.013,t:0.261):0.036):0.061,u:0.229):0.141,(v:0.271,w:0.13):0.165):0.077,(x:0.208,y:0.336):0.161):0.314,(z:0.602,a:0.411):0.151):0.146):0.544,a:0.989):0.128,(((((((((((((b:0.08,c:0.242):0.041,d:0.113):0.018,e:0.125):0.041,f:0.103):0.035,g:0.065):0.056,h:0.132):0.072,i:0.148,(j:0.206,k:0.131):0.033):0.118,l:0.388):0.154,m:0.828):0.136,n:0.95):0.276,(o:0.348,(p:0.141,q:0.135):0.239):0.276):0.07,(r:0.0,s:0.0):0.627):0.382,((((((t:0.126,u:0.07):0.038,v:0.101):0.088,((w:0.0,x:0.07):0.07,(y:0.0,z:0.0):0.19):0.048):0.046,((a:0.05,b:0.0,c:0.0):0.188,((((d:0.18,e:0.043):0.016,(f:0.0,g:0.045):0.02):0.02,h:0.0):0.055,(i:0.0,j:0.0):0.21):0.024):0.082):0.221,(((((k:0.0,l:0.0):0.124,m:0.115):0.169,((n:0.096,o:0.036):0.053,p:0.051):0.128):0.239,q:0.288):0.286,r:0.259):0.133):0.182,(s:0.096,(t:0.022,u:0.056):0.04):0.699):0.455):0.112):0.179,((((((v:0.378,w:0.194):0.223,(x:0.27,(y:0.069,z:0.083):0.198):0.069):0.076,a:0.434):0.012,b:0.368):0.318,((c:0.0,d:0.04):0.241,(e:0.084,f:0.128):0.038):0.389):0.623,((((g:0.229,(h:0.049,h:0.0):0.131):0.305,i:0.544):0.044,(j:0.0,k:0.0):0.33):0.563,(l:0.286,m:0.365):0.879):0.209):0.311)" 293_Wagstaff&Breitwieser_2004_SystBot "Wagstaff, S. J., and I. Breitwieser. 2004. Phylogeny and classification of Brachyglottis (Senecioneae, Asteraceae): an example of a rapid species radiation in New Zealand. 2004. Syst. Botany 29:1003-1010." 49 3 "trnK, matK & ITS" cpDNA & nuDNA 1706 Neighbor Joining GTR+I+G 0.18 0.01 0.055555556 substitutions/site Magnoliophyta 31 -1.220158381 1.012804206 . . . "((((((((boavitt:0.043,southlandica:0.056,bellidioides:0.051):0.081,(compacta:0.04,greyi:0.04):0.066,(recurva:0.045,sinclairii:0.2):0.089,perdicioides:0.201):0.036,pulvinaris:0.106):0.036,((lineuris:0.0,sulicina:0.0):0.09,brunonis:0.188):0.05,sciadophila:0.28):0.034,(cassinioides:0.112,huntii:0.083):0.082,(arborescens:0.089,repania:0.087):0.042,bacchariodes:0.141,kirkii:0.135):0.0,(claeugnifolia:0.107,scorzoneroides:0.167):0.001):0.045,adamsii:0.083):0.213,((((((S_dunealineasis:0.079,S_quadridentatus:0.062):0.067,S_rufiglandulosus:0.16):0.032,S_glaucophyllus:0.163):0.06,(S_lautus:0.183,S_vulgaris:0.207):0.036):0.036,(S_glomerutus:0.066,S_minimus:0.029):0.148):0.289,S_jacobeca:1.166):0.235);" 294_Weckstein_2005_Auk "Weckstein, J. D. 2005. Molecular phylogenetics of the Ramphastos toucans: Implications for the evolution of morphology, vocalizations, and coloration. Auk 122:1191-1209." 100 4 "cyt b, COI, ND2" mtDNA 2468 Maximum Likelihood GTR+I+G 0.246 0.01 0.040650407 substitutions/site 0.0115 Chordata 10 -0.697063623 0.807307693 0.274501952 0.009418915 5.419317846 "((((((vitelinus:0.453,brevis:0.395):0.141,vitelinus:0.521):0.73,dicolorus:0.93):0.166,sulfuratus:0.909):0.208,((culverei:0.059,tucanus:0.092):0.554,(swainsoni:0.149,ambiguus:0.219):0.439):0.376):0.464,toco:1.453);" 296_Wilson_etal_2004_PRSLB "Wilson, A. B., M. Glaubrecht, and A. Meyer. 2003. Ancient lakes as evolitionary reserviors: evidence from the thalassoid gastropods of Lake Tanganyika. Proc. Roy. Soc. Lond., B 271, 529-538." 100 2 16S mtDNA 460 Neighbor Joining K2P 46.7 80 1.713062099 Million years 1 Mollusca 9 -0.525161736 0.239362272 0.049893162 0.000355618 33.57601714 "(((nassa:5.1,grandis:5.1,littoralis:5.1,nassa:5.1,littoralis:5.1):4.7,smithi:10.0):10.7,(arenarum:12.2,(locardiana:2.4,spinulosa:2.4):5.4):8.6);" 297_Zhang_etal_2001_AJB "Zhang, L. -B., H. P. Comes, and J. W. Kadereit. 2001. Phylogeny and quaternary history of the European montane/alpine endemic Soldanella (Primulaceae) based on ITS and AFLP variation. Amer. J. Bot. 88:2331-2345." 88 5 "ITS," nuDNA 654 Neighbor Joining K2P 2.9 0.01 0.003448276 substitutions/site 0.00305 Magnoliophyta 14 -4.10975965 0.065528525 0.041229423 0.000141655 27.92891576 "((minima:23.7,(pusilla:20.9,alpina:22.0):1.6):0.6,((((((montana:13.3,angusta:14.9):1.7,((rugosa:12.0,creodoxa:13.0):0.4,marmarostrssiensis:15.1):0.3):0.2,(hungarica:16.8,major:19.7):0.8):1.5,carpatica:24.2):1.8,(chrysostichta:10.0,rhodpsoa:13.2):4.9):1.1,pindicola:22.9):3.5);" 298_Braun_etal_2005_JMamm "Braun, J. K., R. A. VanDenBussche, P. K. Morton, and M. A. Mares. 2005. Phylogenetic and biogeographic relationships of mouse opossums Thaylamys (Didelphimorphia, Didelphidae) in southern south America. Journal of Mammalogy 86:147-159." 100 2 cyt b mtDNA 402 Maximum Likelihood HKY+I+G 2.6 0.01 0.003846154 substitutions/site 0.0115 Chordata 7 -1.743455412 0.122927232 0.090128105 0.001624615 11.84573626 "((venustus_N:25.9,venustus_S:20.4):8.2,(pusillus:24.0,((elegans_Peru:21.1,elegans_Chile:18.7):3.1,(pallidior_N:8.4,pallidior_S:9.9):7.2):3.1):16.1);" 300_Schwenk_etal_2000_PRSLB "Schwenk, K., D. Posada, and P. D. N. Herbert. 2000. Molecular systematics of European Hyalodaphnia: the role of the contemporary hybridization in ancient species. Proc. Roy. Soc. Lond., B 267:1833-1847." 100 2 COI mtDNA 543 Maximum Likelihood F81+G 4.1 0.1 0.024390244 substitutions/site 0.0115 Arthropoda 8 0.47917768 1.518279747 0.060191489 0.000603836 24.09862152 "((((men:0.0,gal:0.0):3.9,cuc:4.7):5.5,((ros:0.0,hya:0.0):2.9,den:3.2):3.9):4.8,(lon:9.8,umb:7.3):1.0);" 301_Goetze_2003_PRSLB "Goetze, E. Cryptic speciation on the high seas; global phylogenetics of the copepod family Euclanidae. Proc. Roy. Soc. Lond., B 270:2321-2331." 100 3 16S mtDNA 367 Maximum Likelihood p-dist 6.9 0.027247956 0.003948979 substitutions/site 0.0115 Arthropoda 5 -1.829126876 0.031720476 0.059593693 0.001183803 12.41782201 "((nasutus:18.7,(gigas:17.0,nasutus:25.3):6.7):8.8,(rostrifrons:29.0,cornutus:30.7):10.4);" 302_MillerButterworth_etal_2005_JMamm "Miller-Butterworth, C. M., G. Eick, D. S. Jacobs, M. C. Schoeman, and E. H. Harley. 2005. Genetic and phenotypic differences between south African long-finfered bats, with global minopterine phylogeny. Journal of Mammalogy 86:1121-1135." 61 5 cyt b mtDNA 525 Maximum Likelihood GTR+I+G 2.7 0.05 0.018518519 substitutions/site 0.0115 Chordata 9 -1.64049955 0.109097166 0.093333331 0.001244444 14.90036271 "((schreibersii:7.2,(macrocneme:2.0,australis:2.5):2.0):1.6,((natalensis:2.7,(((fraterculus:3.1,inflatus:3.3):2.0,spp:3.5):1.0,manavi:1.7):2.9):2.6,schreibersii:3.4):5.9);" 303_Mayer&vonHelversen_2001_PRSLB "Mayer, F. and O. von Helversen. 2001. Cryptic diversity in European bats. Proc. Roy. Soc. Lond., B 268:1825-1832." 100 2 ND1 mtDNA 600 Maximum Likelihood HKY+I+G 54.2 0.1 0.001845018 substitutions/site 0.0115 Chordata 24 -4.61838785 0.228288445 0.264212011 0.00317309 5.23035028 "(((((((a:9.4,b:9.1):10.8,c:21.7):5.2,((d:16.5,e:18.9):5.0,f:22.0):4.5):1.2,g:27.3):1.9,(h:27.1,i:29.6):1.2):0.7,((j:1.9,k:1.2):11.2,l:14.4):17.9):4.8,(((((m:23.5,((n:3.6,o:4.0):13.9,p:16.1):3.5):1.9,(q:20.7,r:17.9):2.3):0.2,((s:23.2,t:20.5):3.0,u:22.8):1.1):0.5,v:25.2):1.7,(w:20.0,x:22.1):4.0):3.8);" 305_Turgeon_etal_2005_AmNat "Turgeon, J., R. Stoks, R. A. Thum, J. M. Brown and M. A. McPeek. 2005. Simultaneous Quaternary radiations of three damselfly clades across the Holarctic. Amer. Natur. 165:E78-E107." 93 1 COI mtDNA 862 Neighbor Joining GTR+I+G 1 1 1 substitutions/site 0.0115 Arthropoda 38 4.96043722 3.861289639 0.274683397 0.00209586 15.40157286 "((Enov:0.144676,((((Ecir:0.005019,(Eris:0.001536,(Edes:0.001536,Ecya:0.001536):0):0.003483):0.009713,((Eanx:0.000865,Ecla:0.000865):0.005087,((((Ebor:0.002063,Ever:0.002063):0,Elat:0.002063):0.000959,((Erec:0,Emin:0):0.003022,(Edav:0.00215,Eebr:0.00215):0.000873):0):0.002929,Ehag:0.005952):0):0.00878):0.027665,Edur:0.042396):0.027871,(((((Eann:0.002411,Edou:0.002411):0,Easp:0.002411):0,Epra:0.002411):0.000682,(Eciv:0.002467,Ecar:0.002467):0.000625):0.002356,Egem:0.005448):0.064819):0.074409):0.032442,((((Eant:0.087174,(Ediv:0.058554,(Epal:0.00132,Etra:0.00132):0.057234):0.02862):0.032757,(Edae:0.119931,(Eexs:0.061173,Ewee:0.061173):0.058758):0):0.034601,Ebas:0.154532):0.015235,(((Econ:0.002203,Edub:0.002203):0,Epic:0.002203):0.02317,((Epol:0.004965,Esig:0.004965):0.016761,(Esul:0.000609,Eves:0.000609):0.021117):0.003647):0.144394):0.007351);" 306_Stoks&McPeek_2006_AmNat "Stoks, R., and M. A. McPeek. 2006. A tale of two diversifications: reciprocal habitat shifts to fill ecological space along the pond permanence gradient. Amer. Natur. 168:S50-S72." 81 1 COI mtDNA 862 Neighbor Joining GTR+I+G 1 1 1 substitutions/site 0.0115 Arthropoda 10 0.791422169 1.394977293 0.282851512 0.010000622 5.942467391 "(congener:0.068338,((((disjunctus:0,rectangularis:0):0.009335,unguiculatus:0.009335):0.005216,((dryas:0,stultus:0):0.005664,forcipatus:0.005664):0.008887):0.041255,((eurinus:0.050015,inawualis:0.050015):0.003197,vigilax:0.053211):0.002594):0.012533);" 307_Baldwin&Sanderson_1998_PNAS "Baldwin, B. G., and M. J. Sanderson. 1998. Age and rate of diversification of the Hawaiian silversword alliance (Compositae). Proc.Nat. Acad. Sci., USA 95:9402-9406." 89 1 ITS nuDNA 643 Maximum Likelihood HKY85+G 3.912 15 3.834355828 Million years 1 Magnoliophyta 25 0.634761196 1.13850019 0.504109589 0.011048977 5.297761694 "(((gymnoxiphium:0.982,(latifolia:0.927,(paleata:0.238,taillardioides:0.238):0.694):0.075):0.359,((((menziesii:0.184,reticulata:0.184):0.165,(arborea:0.191,scabra:0.191,(ciliolata:0.090,ciliolata:0.090):0.101):0.151):0.317,(herbstobatae:0.0,sherffiana:0.0):0.661):0.562,(laevigata:0.566,(imbricata:0.466,(plantaginea:0.125,plantaginea:0.125,plantaginea:0.125,microcephala:0.125):0.342,(laxi:0.225,laxi:0.225,pauciflorula:0.225,(knudsenii:0.086,knudsenii:0.086):0.139):0.237):0.103):0.664):0.141):0.025,(caliginis:0.091,sandwicense:0.091):1.287);" 308_McKenna&Farrell_2006_PNAS "McKenna, D. D., and B. D. Farrell. 2006. Tropical forests are both evolutionary cradles and museums of leaf beetle diversity. Proc.Nat. Acad. Sci., USA 103:10947-10951." 47 2 COI * ITS mtDNA & nuDNA 2200 Bayesian GTR+I+G 80.7 60 0.743494424 Million years 1 Arthropoda 83 -4.94161691 0.532272562 0.03146492 1.22227E-05 64.21856396 "((((((((((((((immaculata:23.7,ornatrix:23.7):4.4,(marginella:23.7,nevermanni:23.7):4.4):1.3,(((alternans:5.3,luctuosa:5.3):12.9,quadrilineata:18.5):6.9,instabilis:25.1):3.2):5.7,bella:35.1):1.6,suaveola:37.1):5.0,((apicata:19.0,stenosoma:19.0):11.4,sp136:30.9):11.0):15.0,((((antennalis:2.2,flava:2.2):7.1,lepida:9.4):18.6,distincta:28.4):5.5,distincta:34.6):23.3):10.0,princeps:68.8):2.4,((((erichsonii:4.7,erichsonii:4.7):9.4,erichsonii:14.1):21.0,erichsonii:35.5):29.3,pulchella:65.4):5.5):0.6,(((fenistrata:17.4,fenistrata:17.4):34.1,(heliconiae:16.7,heliconiae:16.7):34.5):2.3,(championi:49.4,(gratiosa:31.3,((partita:10.0,bifasciata:10.0):8.4,reventazonica:18.4):12.9):17.9):4.3):17.8):2.1,(dilaticollis:29.8,(erichsonii:11.8,mauliki:11.8):18.0):45.2):5.4,(((A_impurum:5.1,A_semnicircularum:5.1):48.0,D_strandi:53.1):15.9,((dilaticollis:32.3,dilaticollis:32.3):8.9,sp089:42.2):27.0):11.0):2.5,(((((((((((discoidalis:3.5,deficiens:3.5):16.4,histrionica:20.3):13.0,histronica:33.3):4.2,trivittaia:37.5):3.0,suturalis:40.5):10.0,(fulvipes:32.0,sp181:32.0):19.1):5.1,((((congener:7.0,sallei:7.0):5.1,pretiosa:12.1):22.3,flavipennis:34.4):17.0,(tertaspilota:4.6,trimaculata:4.6):47.7):4.1):1.4,histro:58.8):5.2,(((((dorsalis:25.3,sp091:25.3):29.4,((((schmidti:4.3,uhmanii:4.3):14.4,tenelia:18.7):30.7,(fulvolimbata:33.4,furicollis:33.4):16.3):3.9,sp083:54.0):0.8):3.7,sp124:58.8):4.0,S_sp:63.2):0.8,(stevensi:24.5,stevensi:24.5):39.5):0.3):7.4,sagittifera:72.2):4.3,lalli:76.9):6.2):4.9,((((aequilata:72.8,(sp113:67.4,((sp114:42.2,cyanea:42.2):12.3,I_thorcicum:54.4):12.6):5.1):3.9,((aequilata:64.0,P_columbica:64.0):8.4,lata:73.0):3.5):3.0,I_rufiventre:79.6):0.9,((D_sp_175:11.1,costaricensis:11.1):61.2,irregularis:63.3):7.9):7.4);" 309_Berendonk_etal_2003_Evol "Berendonk, T. U., T. G. Barraclough and J. C. Barraclough. 2003. Phylogenetics of pond and lake lifestyles in Chaoborus midge larvae. Evol. 57:2173-2178." 100 2 COI mtDNA 1000 Maximum Likelihood HKY Atrhropoda 10 -3.094882782 0.305008856 0.117852711 0.001736158 8.038949275 "(((((((astictopus:0.058,punctipennis:0.056):0.016,albatus:0.075):0.020,flavicans:0.12,crystallinus:0.1):0.004,(americanus:0.002,pallidus:0.003):0.088):0.009,obscuripes:0.089):0.019,cooki:0.084):0.05,trivitattus:0.034);" Baker_etal_2005_PNAS "Baker, A. J., L. J. Huynen, O. Haddrath, C. D. Millar, and D. M. Lambert. 2005. Reconstructing the tempo and mode of evolution in an extinct clade of birds with ancient DNA: The giant moas of New Zealand. Proceedings of the National Academy of Science, USA 102:8257–8262." 100 1 control region mtDNA 658 Bayesian GTR+I+G. 1.239 5 4.03551251 Million years 1 Chordata 12 -2.125771134 0.051838988 0.109636315 0.001202012 15.44811003 "((((1:1.119,2:1.119):0.51,(3:1.14,4:1.14):0.475,5:1.6):0.798,((6:1.035,7:1.035):0.36,8:1.38):1.018):1.394,((9:1.28,10:1.28,11:1.28):0.773,12:2.079):1.787);" Baum_etal_1998_SystBiol "Baum, D. A., R. L. Small, and J. F. Wendel. 1998. Biogeography and floral evolution of baobabs (Adansonia, Bombacaceae) as inferred from multiple data sets. Syst. Biol. 47:181-207." 100 4 ITS nuDNA 787 Maximum Likelihood HKY+J252G 3.668 0.09789 0.026687568 substitutions/site 0.00305 Magnoliophyta 8 -0.199474091 0.782864437 0.221769902 0.008196982 6.358896411 "(gibbosa:0.72,(digitata:0.654,((grandidieri:0.143,suarezensis:0.143):0.162,rubrostipa:0.288,((madagascariensis:0.105,perrieri:0.112):0.038,za:0.123):0.16):0.371):0.073);" Chiba_1999_Evol "Chiba, S. 1999. Accelerated evolution of land snails Mandarina in the oceanic Bonin Islands: evidence from mitochondrial DNA sequences. Evol. 53:460–471." 100 5 "16S, 12S" mtDNA 1240 Neighbor Joining K2P 0.334 0.01 0.02994012 substitutions/site 0.0115 Mollusca 13 -0.436824644 0.834053126 0.279771468 0.007115643 6.550357219 "((((((((aureola:0.121,polita:0.149):0.078,hahajimana:0.494):0.385,(exoptata:0.706,conus:0.499,ponderosa:0.448):0.116):0.1,hahajimana:0.978):0.218,(chichijimana:0.219,mandarina:0.188):1.638):0.073,(trifasciata:1.504,hirasei:1.786):0.081):0.345,suenoae:1.886):0.326,anijimana:2.772);" Comes&Abbott_2001_Evol "Comes, H. P., and R. J. Abbott. 2001. Molecular phylogeography, reticulation, and lineage sorting in Mediterranean Senecio sect. Senecio (Asteraceae). Evol. 55:1943–1962." 75 5 ITS nuDNA 487 Maximum Likelihood TrN+G 0.167 0.005 0.02994012 substitutions/site 0.00305 Magnoliophyta 23 2.920032222 2.898190984 0.276541783 0.003641684 14.98236889 "((((((((glaucus:0.0,hesperidium:0.0):0.067,rupesris:0.076,petraeus:0.0,rodriguezii:0.061,squalidus:0.069,(gallicus:0.238,chrysanthomerifolius:0.044):0.027,squalidus:0.013,leucanthermifolis:0.0):0.068,(rupestris:0.11,(glaucus:0.136,flavus:0.222):0.108):0.023):0.069,aethnenis:0.0):0.397,(vernalis:0.344,(vulgaris:0.432,rupestris:0.178):0.084):0.336):0.064,((viscosus:0.21,nebrodensis:0.218):0.119,(tividus:0.085,sylvaticus:0.14):0.024):0.077):0.406,flavus:3.734):0.446,aegyptius:0.29);" Donald_etal_2005_Evol "Donald, K. M., M. Kennedy, and H. G. Spencer. 2005. Cladogenesis as the result of long-distance rafting events in south Pacific topshells (Gastropoda: Trochidae). Evol. 59:1701–1711." 96 2 "16S, COI & actin" mtDNA & nuDNA 2169 Maximum Likelihood GTR+I+G 0.276 0.05 0.18115942 substitutions/site Mollusca 19 0.492522137 1.035833982 . . . "((((((((D_arida:0.578,D_coracina:0.693):0.145,D_zelandica:0.365):0.038,(D_nigerrima:0,D_crusoeana:0):0.310):0.052,D_bicanaliculata:0.391):0.042,((D_subrostrata:0.201,M_aethiops:0.200):0.461,A_concamerata:0.461):0.052):0.152,(D_samoaensis:0.230,D_radula:0.405):0.230):0.460,((((A_rudis:0.037,A_constricta:0):0.067,A_porcata:0.088):0.261,A_brevis:0.208):0.650,A_diminuta:1.567):0.619):0.618,((A_odontis:0.090,A_crinita:0.028):0.372,A_adelaidae:0.295):0.983);" Douady_etal_2003_PNAS "Douady, C. J., F. Catzeflis, J. Raman, M. S. Springer, and M. J. Stanhope. 2003. The Sahara as a vicariant agent, and the role of Miocene climatic events, in the diversification of the mammalian order Macroscelidea. Proc.Nat. Acad. Sci., USA 100:8325–8330." 60 3 "12S, valine tRNA, 16S rRNA, vWF IRB" mtDNA and nuDNA 4065 Bayesian F84+G 0.505 10 19.8019802 Million years 1 Chordata 4 -1.117053985 0.017907861 0.026274714 0.00034518 23.79207921 "((myurus:0.637,edwardii:0.637):0.548,(intufi:0.804,rufescens:0.804):0.414);" Drovetski_2002_SystBiol "Drovetski, S. V. 2002. Molecular phylogeny of grouse: Individual and combined performance of W-linked, autosomal, and mitochondrial loci. Syst. Biol. 51:930-945." 100 5 "AG3I3, ASWI2,WPG, Control region" mtDNA and nuDNA 3250 Maximum Likelihood GTR+I+G 0.163 0.005 0.030674847 substitutions/site Chordata 21 -0.534454082 0.898802116 . . . "((umbellus:1.828,(bonasia:0.389,sewerzowi:0.456):0.947):0.179,((((urophasianus:0.237,minimus:0.306):0.526,((obscurus:0.205,fuliginosus:0.207):0.275,((cupido:0.0,(attwateri:0.0,pallidicinctus:0.109):0.065):0.058,phasianellus:0.104):0.728):0.19):0.281,(leucurus:0.459,(lagopus:0.529,mutus:0.44):0.358):0.234):0.069,(((canadensis:0.134,franklinii:0.209):0.555,falcipennis:0.678):0.176,((tetrix:0.316,mlolosiewiczi:0.202):0.215,(parvirostris:0.186,urogallus:0.39):0.193):0.326):0.113):0.386);" Glor_etal_2003_Evol "Glor, R. E., J. J., Kolbe, R. Powell, A. Larson, and J. B. Losos. 2003. PHylogenetic analysis of ecological and morphological diversification in Hispaniolan trunk-ground anoles (Anolis cybotes group). Evolution 57:2383–2397." 100 3 "ND2, tRNAMet, tRNAIle, tRNATrp, tRNAAla, tRNAAsn, tRNACys, tRNATyr, ND1 and COI" mtDNA 1921 Bayesian HKY+G+I 0.056 0.005205622 0.092957537 substitutions/site 0.0115 17 -3.140867024 0.181036831 0.156270145 0.001628024 10.27098195 Chordata Johns&Avise_1998_Evol "Johns, G. C., and J. C. Avise. 1998. Tests for ancient species flocks based on molecular phylogenetic appraisals of Sebastes rockfishes and other marine fishes. Evol. 52:1135–1146." 100 2A cytb mtDNA 855 Maximum Likelihood HKY 4.628 0.16 0.034572169 substitutions/site 0.0115 Chordata 28 -2.440994802 0.518591746 0.403403848 0.006259026 5.634641154 "(((((((chrysomelas:0.312,caurinis:0.312):0.034,atrovirens:0.344):0.247,rastrelliger:0.576):0.266,(saxicola:0.645,semicinctus:0.645):0.221):0.471,(((((mystinus:0.21,entomelas:0.21):0.552,((melanops:0.19,flavidus:0.19):0.082,serranoides:0.255):0.511):0.26,(((rosaceus:0.236,constellatus:0.236):0.162,(helvomaculatus:0.288,ensifer:0.288,chlorostichtus:0.288):0.101):0.275,(ruricinctus:0.53,rufus:0.53):0.118):0.37,((diploproa:0.603,elongatus:0.603):0.218,((melanostomus:0.703,crameri:0.703):0.081,miniatus:0.778):0.142):0.118,levis:1.007):0.139,ruberrimus:1.123):0.055,maurinus:1.17):0.146):0.166,goodei:1.455):0.409,paucispinis:1.865);" Joy&Conn_2001_SystBiol "Joy, D. A., and J. E. Conn. 2001. Molecular and morphological phylogenetic analysis of an insular radiation in Pacific black flies (Simulium). Syst. Biol. 50:18-38." 100 5 "COI, 12S" mtDNA 1378 Maximum Likelihood GTR+I+G 0.538 0.01 0.018587361 substitutions/site 0.0115 Arthropoda 19 -4.68607402 0.099630276 0.37355397 0.008208386 3.656819807 "(((((((cataractarum:0.976,jnabsium:0.843):0.951,((concludium:1.69,neoviceps:0.726):0.097,(oviceps:2.126,dussertorum:1.756):0.387):0.097):0.263,((connae:1.008,(((((dojyecorium:0.724,fossatiae:0.625):0.451,tahitiense:1.062):0.176,lotii:1.178):0.159,exasperans:1.004):0.305,shannonae:1.123):0.262):0.192,maraaense:1.626):0.211):0.09,lonckei:1.331):0.253,(mesodontium:1.53,middlemissae:0.841):0.228):0.444,clibanarium:1.82):0.501,malardei:2.053);" Kimball_etal_2003_Evol "Kimball, R. T., D. J. Crawford, and E. B. Smith. 2003. Evolutionary processes in the genus Coreocarpus: Insights from molecular phylolgenetics. Evol. 57:52–61." 100 2 ITS nuDNA 652 Maximum Likelihood F81+G 0.211 0.01 0.047393365 substitutions/site Magnoliophyta 7 1.548610058 1.632741807 . . . "((((arizonicus:0.087,(sonoranus:0.038,sanpedroensis:0.049,parthenioides:0.049):0.059):0.054,sonoranus:0.122):0.051,dissectus:0.302):0.555,insularis:0.626);" Moller&Cronk_2001_Evol "Moller, M., and Q. C. B. Cronk. Evolution of morphological novelty: A phylogenetic analysis of growth patterns in Streptocarpus (Gesneriaceae). Evol. 55:918–929." 60 2 ITS nuDNA 743 Maximum Likelihood GTR+I+G. 0.143 0.01 0.06993007 substitutions/site 0.00305 Magnoliophyta 84 1.769006642 1.577676222 0.166387355 0.000337619 22.79238102 "(((nobilis:0.836,((kamerunensis:0.513,elongatus:1.694):0.919,(thysanotus:0.065,kimbozanus:0.041):0.795):0.106):0.016,((((bea_ant:0.538,bea_bea:0.841):0.058,(andohahelensis:0.542,sp:0.045):0.029):0.116,((tanala:0.192,hilsenbergii:0.336):0.346,(thomsonii:0.075,sp:0.0):0.066):0.559):0.82,((saxorun:0.225,(strmandrus:0.025,kirkii:0.074):0.070):0.326,((teitensis:0.16,(ionantha:0.041,(brevipilosa:0.038,nitida:0.079):0.079):0.329):0.423,(pallidiflorus:0.063,(holstii:0.0,glandulosissimus:0.056):0.02,(buchananii:0.086,caulescens:0.034):0.023):0.261):0.084):0.195):0.073):0.208,((itityensis:0.216,macropodus:0.114,itremensis:0.24,papangae:0.444):0.098,(exserius:0.43,(burundianus:0.61,(hildebrandtii:0.349,perreiri:0.82):0.176):0.032,((schliebenii:0.369,(alba:0.0,sp:0.0,bullatus:0.03):0.083):0.344,(nimbicola:0.144,hirticapsa:0.327,((hirtinervis:0.175,(milanjianus:0.155,dolocanthus:0.057):0.023):0.332,((decipiens:0.446,galpinii:0.404):0.072,(((fanniniae:0.191,pulillus:0.04,davyi:0.1):0.165,(((pole_evansii:0.104,dunnii:0.07):0.089,(erubescens:0.149,(cyanandrus:0.0,pumilus:0.0):0.071):0.089):0.06,((grandis:0.057,wittei:0.0,cooperi:0.0):0.141,(eylesii:0.032,goetzei:0.032,compressus:0.108,solenanthus:0.061,(kungwensis:0.022,bindseilii:0.0):0.032):0.036):0.079):0.268):0.044,(bolusii:0.288,(porphyrostachys:0.193,(haygarthii:0.126,candidus:0.177,(((confusus:0.052,wnedlandii:0.139):0.032,(trabeculatus:0.219,(molweniensis:0.117,((silvaticus:0.051,pentherianus:0.078):0.040,(poly:0.046,prolixus:0.101):0.078):0.024):0.035):0.023):0.023,(kentaniensis:0.0,(cyaneus:0.055,meyeri:0.0,fasciatus:0.0,montigena:0.085):0.031,(bauderii:0.0,rexii:0.058,primulifolius:0.0,(johannis:0.042,modestus:0.069,prim:0.0):0.033):0.028):0.03):0.109):0.038):0.051):0.088):0.095):0.033):0.023):0.024):0.033):0.04):0.084);" Near&Benard_2004_Evol "Near, T. J., and M. F. Bernard. Rapid allopatric speciation in logperch darters (Percidae: Percina). Evol. 58:2798–2808." 100 3 "cytb, ND2" mtDNA 2187 Bayesian GTR+I+G 5.585 5 0.895255148 Million years 1 Chordata 10 0.281487266 0.88943962 0.451244761 0.025452729 4.200586114 "(rex:4.695,(jenkinsi:3.332,(burtoni:2.294,(carbonaria:1.176,((macrolepida:0.761,(suttkusi:0.639,caprodes:0.644):0.134):0.132,(nebulosa:0.823,(austroperca:0.483,kathae:0.481):0.338):0.082):0.273):1.121):1.039):1.356);" Parker&Rissing_2002_Evol "Parker, J. D., and S. W. Rissing. 2002. Molecular evidence for the origin of workerless social parasites in the ant genus Pogonomyrmex. Evol. 56:2017–2028." 53 5 cytb mtDNA 711 Neighbor Joining TrN+G 0.539 0.05 0.092764378 substitutions/site 0.0115 Arthropoda 19 0.070897278 1.114062819 0.097224259 0.000556033 28.544917 "((((((((((((anergismus:0.224,colei:0.186):0.133,barbatus1:0.189):0.326,(apache:0.251,desertorum:0.243):0.131):0.024,(rugosus1:0.236,barbatus2:0.125):0.335):0.156,rugosus2:0.656):0.151,tenuispina:1.123):0.450,((occidentalis:0.270,salinus:0.287):0.572,subnitidus:0.845):0.822):0.089,bicolor:1.222):0.140,((californicus:0.323,maricopa:1.059):0.217,magnacanthus:1.076):0.354):0.467,anzensis:1.266):0.930,huachucanus:2.200):0.700,imberbiculus:4.015);" Quek_etal_2004_Evol "Quek, S.-P., S. J. Davies, T. Itinon, and N. E. Pierce. 2004. Codiversification in the ant-plant mutualism: stem texture and the evoltuion of host use in Crematogaster(Formicidae:Myrmicinae) inhabitants of Macaranga (Euforbiaceae). Evol. 58:554–570." 88 3 COI mtDNA 565 Bayesian GTR+I+G 0.063 0.008849558 0.140469167 substitutions/site 0.0115 Arthropoda 10 -2.501691441 0.152293185 0.150811945 0.00284303 8.590806063 "(((((((((h:0.236,j:0.176):0.031,k:0.272):0.118,g:0.488):0.061,f:0.243):0.154,c:0.427):0.048,d:0.383):0.07,e:0.292):0.329,b:0.303):0.252,a:0.635);" Ruber_etal_1999_PNAS "Ruber, L., E. Verheyen, and A. Meyer. 1999. Replicated evolution of trophic specializations in an endemic cichlid fish lineage from Lake Tanganyika. Proc.Nat. Acad. Sci., USA 96:10230–10235." 100 1 "cyt, and control" mtDNA 701 Neighbor Joining 0.673 0.02 0.029717682 substitutions/site 0.0115 Chordata 6 -2.438484202 0.034282758 0.197335543 0.009735329 4.177595449 "(A:1.828,(B:1.256,(C:1.271,(D:0.828,(E:1.23,F:1.174):0.072):0.067):0.178):0.091);" Sato_etal_1999_PNAS "Sato, A., C. O'Huigin, F. Figueroa, P. R. Grant, B. R. Grant, H. Tichy, and J. Klein. 1999. Phylogeny of Darwin’s finches as revealed by mtDNA sequences. Proc.Nat. Acad. Sci., USA 96:5101–5106." 93 5 "cyt, and control" mtDNA 2049 Neighbor Joining TrN 3.669 0.02 0.005451077 substitutions/site 0.0115 Chordata 13 0.527767756 1.176726863 1.429935501 0.185883231 1.615967827 "((((((magnirostris:0.19,difficilis:0.361,scandens:0.332):0.078,(conirostris:0.332,fortis:0.332):0.09):0.111,fuliginosa:0.852):0.646,(inornata:2.055,((pallida:0.696,psittacula:0.286):0.225,(pauper:0.656,parvulus:0.548):0.203):0.123):0.182):0.692,crassirostris:3.022):1.201,olivacea:3.016);" Steppan_etal_1999_Evol "Steppan, S. J., M. R. Akhverdyan, E. A. Lyapunova; D. G. Fraser, N. N. Vorontsov, R. S. Hoffmann, and M. J. Braun. 1999. Molecular Phylogeny of the Marmots (Rodentia: Sciuridae): Tests of Evolutionary and Biogeographic Hypotheses. Syst. Biol. 48:715-734." 100 5 cytb mtDNA 1140 Maximum Likelihood GTR+I+G. none Chordata 14 -3.076044038 0.213241844 . . . "(((((sibirica:1.144,himalayana:1.284):0.337,camtschatica:1.805):0.482,(bobak:1.151,baicacina:1.32):0.394):0.255,(((caudata:0.921,menzbieri:1.328):0.734,broweri:2.203):0.23,marmota:2.129):0.1,monax:2.213):0.561,(((callgata:0.219,vancouverensis:0.23):0.753,olympus:1.521):0.213,flaviventris:1.147):1.048);" Williams&Reid_2004_Evol "Williams, S. T., and D. G. Reid. 2004. Speciation and diversity on tropical rocky shores: A global phylogeny of snails of the genus Echinolittorina. Evol. 58:2227–2251." 100 4 "12s, CO1, 28s" mtDNA and nuDNA 2949 Bayesian GTR+I+G 3.665 19 5.184174625 Million years 1 Mollusca 49 -2.384213277 0.686147785 0.101551976 0.000219421 22.31784645 "(((lineolata:3.285,peroviasa:3.285):0.67,((sarteianae:2.257,((parcisida:0.063,luscolineata:0.063):1.541,(albicannata:1.404,(purcata:0.694,atrata:0.694):0.715):0.18):0.652):1.505,(punctata:3.461,(((angustor:2.019,peniciliata:2.019):0.331,(interrupta:1.996,(aspera:0.17,(dubiosa:0.119,tenuistrate:0.119):0.055):1.805):0.352):0.486,((rosei:1.521,(apicina:0.066,paydentus:0.066):1.445):1.014,((conspersa:0.717,modesta:0.717):0.892,ziczac:1.615):0.907):0.302):0.64):0.282):0.204):0.347,((galapageiensis:3.335,((vernega:1.802,tuberculata:1.802):0.945,(graeosa:1.29,(terleriae:0.344,trilans:0.344):0.946):1.451):0.584):0.746,((melearis:0.595,mespilium:0.595):3.069,((radiata:2.496,antica:2.496):0.193,(((paccua:1.878,(satalensis:0.968,subrodiosa:0.968):0.914):0.55,(sundaica:2.329,trochvoidea:2.329):0.105):0.137,((quadricincta:1.437,((quadricincta:0.605,leucosticta:0.605):0.56,(australis:0.97,quadricincta:0.97):0.208):0.257):0.619,((teejeensis:0.568,melanacme:0.568):0.706,((novezelandiae:0.604,indua:0.604):0.528,(cenerea:0.655,(hawaiiensis:0.566,(millegrana:0.049,robusticulata:0.049):0.518):0.1):0.469):0.142):0.78):0.523):0.115):0.965):0.419):0.23);" Xiang_etal_2005_Evol "Xiang, Q.-Y., S. R. Manchester, D. T. Thoma, W. Zhang, and C. Fan. 2005. Phylogeny, biogeography, and molecular dating of cornelian cherries (Cornus, Cornaceae): Tracking Tertiary plant migration. Evol. 59:1685–1700." 100 1 "rbcL, matK" cpDNA 2976 Bayesian GTR+I+G 0.388 0.005 0.012886598 substitutions/site Magnoliophyta 14 -1.146553007 0.460339868 . . . "((((((kousa:0.390,capitata:0.084):0.444,disciflora:0.577):0.069,florida:0.185):1.472,canadensis:2.313):0.403,((walteri:0.600,controversa:0.735):0.535,oblonga:0.964):0.159):0.178,((volkensii:0.365,(((mas:0.458,officinalis:0.162):0.126,eydeana:0.498):0.238,chinensis:0.261):0.188):0.105,sessilis:0.321):0.819);" GTR+I+G GTR+I+G TrN+I+G GTR+I+G+penalizedlikelihood GTR+I+G HKY+G+I GTR+G+I GTR+G TrN+G GTR+G+I K3STf+G+Iwithmol.Clock TrNef+G 4categories(3sites+tRNA GTR+I+G. 2:1Ti:Tv HKY2nTi:TV GTR+G+I GTR+G GTR+G+I GTR+I+G. HKY-G GTR+I+G. GTR+G F84+G8 unk Tamura-Nei