#NEXUS Begin taxa; dimensions ntax=46; taxlabels ALEC LEI MEGA AFCO ALC ALR ARAR BAM CAW CHP COJ COVI CRAX CRO CYM FAC GGA GLA GSO GUTT GVA LIMP LINO LNY LSW MEG NUM OREO ORT PACR PAM PBI PCH PEM PGE PHCO PIN PMA PPX PUCM RORO SEL SRE TBL TTE TYM ; End; [! ############ ## README ## ############ Trees from Kimball and Braun (2014) You may wish to rename this file with the extension .nex or .tre This NEXUS treefile will execute in PAUP* and it can be displayed using FigTree. If you have difficulties displaying the treefile use one of those programs, which can be downloaded from the following websites: FigTree -- https://github.com/rambaut/figtree/releases PAUP* -- https://paup.phylosolutions.com/ All trees are ML trees estimated using PAUP* 4.0b10 (Swofford et al. 2003). In some cases there were multiple equally optimal trees. The strict consensus is presents as the topology in those cases (indicated with _cons followed by the number of equally optimal topologies). In all cases the topology for Gallus was identical in all trees, although it was unresolved (i.e., the relevant branch had a length close to zero that was collapsed by PAUP*) in six cases. Three of the trees with a polytomy in Gallus were compatible with the Tiley et al. topology (see below). The full set of taxon names is presented at the end of this README section. Topologies within Gallus: Locus Topology ----- -------- CRYAA (G,(V,(L,S))); CHRNG (G,(V,L,S)); ALDOB (V,(G,L,S)); - consistent with Tiley et al. topology FGB (V,(L,(G,S))); CALB1 (G,(V,(L,S))); CLTC ((G,S),(L,V)); CLTCL1 ((G,S),(L,V)); PCBD1 (V,(L,(G,S))); EEF1 (S,(L,(V,G))); GAPDH (G,(V,(S,L))); HMGN2 (S,L,(G,V)); HSP90B1 ((G,V),(L,S)); SERPIN (V,G,(L,S)); - consistent with Tiley et al. topology OVM (L,(G,V,S)); RHO (V,(G,L,S)); - consistent with Tiley et al. topology Codes for topology within Gallus: V = varius G = gallus L = lafayettii S = sonneratii REFERENCES: Kimball, R. T., & Braun, E. L. (2014). Does more sequence data improve estimates of galliform phylogeny? Analyses of a rapid radiation using a complete data matrix. PeerJ, 2, e361. https://doi.org/10.7717/peerj.361 Swofford DL. 2003. PAUP∗: Phylogenetic analysis using parsimony (∗ and other methods), version 4.0. Sinauer, Sunderland, MA COMPLETE TAXON NAMES: Code Genus_species ---- ------------- ALEC Alectura_lathami LEI Leipoa_ocellata MEGA Megapodius_layardi AFCO Afropavo_congensis ALC Alectoris_chukar ALR Alectoris_rufa ARAR Argusianus_argus BAM Bambusicola_thoracica CAW Catreus_wallichii CHP Chrysolophus_pictus COJ Coturnix_japonica COVI Colinus_virginianus CRAX Crax_rubra CRO Crossoptilon_crossoptilon CYM Cyrtonyx_montezumae FAC Falcipennis_canadensis GGA Gallus_gallus GLA Gallus_lafayetii GSO Gallus_sonneratii GUTT Guttera_pucherani GVA Gallus_varius LIMP Lophophorus_impejanus LINO Lophura_inornata LNY Lophura_nycthemera LSW Lophura_swinhoii MEG Meleagris_gallopavo NUM Numida_gallopavo OREO Oreortyx_pictus ORT Ortalis_vetula PACR Pavo_cristatus PAM Pavo_muticus PBI Polyplectron_bicalcaratum PCH Polyplectron_chalcurum PEM Polyplectron_napoleonis PGE Polyplectron_germaini PHCO Phasianus_colchicus PIN Polyplectron_inopinatum PMA Polyplectron_malacense PPX Perdix_perdix PUCM Pucrasia_macrolopha RORO Rollulus_rouloul SEL Syrmaticus_ellioti SRE Syrmaticus_reevesii TBL Tragopan_blythii TTE Tragopan_temminckii TYM Tympanuchus_phasianellus ] Begin trees; Translate 1 ALEC, 2 LEI, 3 MEGA, 4 AFCO, 5 ALC, 6 ALR, 7 ARAR, 8 BAM, 9 CAW, 10 CHP, 11 COJ, 12 COVI, 13 CRAX, 14 CRO, 15 CYM, 16 FAC, 17 GGA, 18 GLA, 19 GSO, 20 GUTT, 21 GVA, 22 LIMP, 23 LINO, 24 LNY, 25 LSW, 26 MEG, 27 NUM, 28 OREO, 29 ORT, 30 PACR, 31 PAM, 32 PBI, 33 PCH, 34 PEM, 35 PGE, 36 PHCO, 37 PIN, 38 PMA, 39 PPX, 40 PUCM, 41 RORO, 42 SEL, 43 SRE, 44 TBL, 45 TTE, 46 TYM ; [ Codes for trees: ] [ C = Unresolved within Gallus, compatible with Tiley et al. topology ] [ u = Unresolved within Gallus but incompatible with Tiley et al. topology ] tree CRYAA_cons2 = [&U] (1,2,(3,((((((((4,(30,31)),7,((32,(33,35,37)),(34,38))),((5,6),11)),((8,(17,((18,19),21))),((((9,14),(10,(23,24,25)),(36,(42,43))),39),(((16,46),(26,40)),22,(44,45))))),41),((12,28),15)),(20,27)),(13,29)))); [u] tree CHRNG = [&U] (1:0.011605,2:0.025008,(3:0.022914,((((((4:0.013511,(30:0.004885,31:0.001423):0.003054):0.014729,7:0.015070):0.001788,(((((5:0,6:0.001583):0.019723,11:0.036970):0.006294,((32:0,(33:0.003157,37:0):0.001570,35:0.006329,38:0.008047):0.003347,34:0.004614):0.003438):0.001341,((((((9:0.004781,14:0.003177):0.003199,(10:0.009639,((23:0.006439,24:0.004833):0.003135,25:0.006345,36:0.003147):0.001591,(42:0.004864,43:0.009705):0.003094):0.001566):0.005399,39:0.027466):0.005106,((16:0.007912,46:0.018168):0.012122,(26:0.019082,40:0.022345):0.001983):0.006101):0.007275,(22:0.010089,(44:0.009321,45:0.004923):0.005493):0.001011):0.008303,41:0.024329):0.001941):0.007657,(8:0.008772,(17:0.001594,(18:0.006526,19:0.001574,21:0.007960):0.001561):0.007369):0.012534):0.004082):0.001938,(20:0.006740,27:0.008605):0.018100):0.001369,((12:0.009926,28:0.012284):0.011190,15:0.013488):0.034409):0.046905,(13:0.016702,29:0.018606):0.044506):0.060245):0.005668); [C] tree ALDOB = [&U] (1:0.016796,2:0.031400,(3:0.046623,((((((((4:0.009458,(30:0.004278,31:0.002151):0.003449):0.026651,(5:0.004174,6:0):0.031318,(((32:0,33:0,35:0.002244,37:0.002244):0.009094,38:0.002250):0.004489,34:0.006819):0.018509):0.002569,(8:0.032775,((17:0.006305,18:0,19:0.002207):0.004245,21:0.010580):0.005960):0.020020):0.002244,(7:0.008512,11:0.081772):0.002352,41:0.069314):0.001914,((((((9:0.004278,14:0.017809,(23:0.007353,24:0.002116,25:0.004235):0.004914):0.002087,10:0.006413):0.002119,(42:0.010617,43:0.013137):0.008809):0.004354,36:0.013207):0.013404,((16:0.006408,46:0.006428):0.028695,26:0.045546,40:0.026186):0.002164,39:0.068198,(44:0.002116,45:0.002075):0.019282):0.001804,22:0.034841):0.011646):0.013271,((12:0.026480,28:0.045347):0.012912,15:0.021625):0.077692):0.009989,(20:0.013318,27:0.021051):0.034607):0.061045,(13:0.012394,29:0.006492):0.068890):0.085591):0.011032); tree FGB = [&U] (1:0.027119,2:0.021270,(3:0.021221,(((((((((4:0.002743,(30:0.001395,31:0.000696):0.004305):0.030686,7:0.024024):0.001896,(8:0.032863,(((17:0.001597,19:0.000800):0.000795,18:0.003205):0.000802,21:0.002512):0.017127):0.028498):0.002373,((((32:0.003590,35:0.004365):0.000727,(33:0,37:0.003587):0.000712):0.006545,38:0.010246):0.001084,34:0.012096):0.037837):0.000991,(((5:0.001992,6:0.005096):0.043968,11:0.048442):0.010922,(((((((9:0.009214,((10:0.006789,36:0.008426):0.000964,14:0.003407):0.000841):0.001042,(23:0.009297,24:0.007484,25:0.005833):0.003976):0.001907,(42:0.003300,43:0.016074):0.006742):0.014934,40:0.030903):0.000514,39:0.051381):0.000902,((16:0.003350,46:0.009397):0.031840,26:0.031922):0.005338):0.002564,(22:0.017067,(44:0.007571,45:0.008411):0.025337):0.006448):0.024673):0.001197):0.012487,41:0.062783):0.030172,((12:0.025935,28:0.019577):0.015051,15:0.029889):0.069006):0.007471,(20:0.008764,27:0.015124):0.040575):0.056342,(13:0.010211,29:0.014287):0.088411):0.068596):0.009534); tree CALB1 = [&U] (1:0.015162,2:0.006078,(3:0.027358,((((((4:0.010524,30:0.001732,31:0.005215):0.005217,(5:0.001305,6:0.002179):0.024831,7:0.023520,((8:0.021699,(17:0.001723,((18:0,19:0):0.006926,21:0):0.001723):0.005163):0.007290,11:0.030620):0.003320,(((32:0.001739,33:0,37:0):0.003488,38:0.008861):0.005374,(34:0,35:0.003474):0.001647):0.017814):0.001701,((9:0.003452,(10:0.007000,14:0.005211,((23:0.003513,36:0.005330):0.001698,24:0,25:0.008713,(42:0.006931,43:0):0.001724):0.001726):0.001729,(16:0.003487,46:0.001722):0.005256,26:0.022937,(39:0.015943,(44:0.005232,45:0.003465):0.003458):0.001751,40:0.015833):0.001645,22:0.015845):0.012898,41:0.043269):0.003085,(20:0.010729,27:0.021399):0.033903):0.004233,((12:0.015016,28:0.019769):0.011787,15:0.032089):0.030299):0.017183,(13:0.005028,29:0.008892):0.039849):0.045696):0.012041); tree CLTC = [&U] (1:0.018534,2:0.016163,(3:0.032396,(((((((4:0.005529,(30:0.003611,31:0.007791):0.006811):0.022846,((((((9:0.018707,(42:0.010634,43:0.010745):0.004611):0.000333,36:0.008616):0.004553,(((10:0.010664,(23:0.001512,24:0.003568):0.005830):0.003124,14:0.001880):0.003772,25:0.011268):0.003120):0.006345,39:0.025621):0.006973,(22:0.013905,(44:0,45:0.006196):0.010572):0.005056):0.001451,(((16:0.005238,46:0.010197):0.035474,26:0.029330):0.000153,40:0.021715):0.005738):0.008325):0.010063,(((((5:0,6:0.003028):0.021598,11:0.040772):0.013772,(8:0.015662,((17:0.007307,19:0.003341):0.004606,(18:0,21:0):0.010349):0.003286):0.016685):0.009247,(((32:0.001505,35:0.001503):0.001505,33:0.001512,37:0.003013):0.007527,(34:0.009374,38:0.001535):0.001904):0.018540):0.007492,7:0.025225):0.003345):0.010381,41:0.057159):0.010922,((12:0.018422,28:0.018601):0.017659,15:0.025452):0.037711):0.001896,(20:0.015078,27:0.020844):0.041833):0.049806,(13:0.010523,29:0.000382):0.110292):0.129638):0.022313); tree CLTCL1 = [&U] (1:0.018576,2:0.010040,(3:0.027504,((((((4:0.013154,(30:0.002544,31:0):0.007536):0.019060,((5:0,6:0):0.014719,11:0.057169):0.014882):0.002064,(7:0.014000,41:0.075704):0.004116,(8:0.043103,((17:0.010144,19:0.002683):0.002346,(18:0,21:0):0.010643):0.023780):0.026829,(((((9:0.015919,(((10:0.005286,14:0):0.002611,(23:0.007840,24:0.013136,25:0):0.002608,36:0.013493):0.002580,(42:0.005173,43:0.018657):0.005361):0.005295,39:0.046364):0.005412,(16:0.002502,46:0.013430):0.018965):0.005280,(26:0.030196,40:0.041682):0.003118):0.002687,(22:0.021646,(44:0.002589,45:0.005371):0.019250):0.002306):0.007967,((32:0.002542,33:0,35:0,37:0):0.002539,34:0.007716,38:0.010334):0.026323):0.005240):0.017787,((12:0.041136,28:0.029720):0.010611,15:0.036057):0.025998):0.008266,(20:0.026510,27:0.015702):0.026372):0.030588,(13:0.012867,29:0.016193):0.089147):0.140465):0.006328); tree PCBD1 = [&U] (1:0.016300,2:0.025968,(3:0.040959,((((((((4:0.005759,(30:0,31:0):0.005623):0.028758,(((32:0.001944,33:0.003882,35:0.007842,37:0.005866):0.005874,34:0.011794):0.003001,38:0.006777):0.025995):0.002188,(((5:0.003894,6:0.001903):0.041765,11:0.047610):0.017620,7:0.030818):0.001475,(((((((9:0.011810,14:0.005840):0.003873,43:0.015600):0.001936,10:0.017572,((23:0.005959,24:0.011647):0.003905,(25:0.013734,36:0.011916):0.003790):0.001928,42:0.013561):0.003502,((16:0.013642,46:0.009643):0.011097,26:0.027602):0.003735):0.002388,(44:0.002032,45:0.003920):0.023535):0.002028,39:0.035836,40:0.044266):0.001571,22:0.022012):0.015493):0.001856,(8:0.033548,(((17:0,19:0):0.009335,18:0.004154):0.007859,21:0.011978):0.025352):0.013528):0.010574,41:0.097877):0.009737,((12:0.051997,28:0.021291):0.038333,15:0.056287):0.055573):0.009177,(20:0.012344,27:0.013320):0.038427):0.061580,(13:0.013884,29:0.017704):0.072797):0.096690):0.011565); tree EEF1 = [&U] (1:0.014546,2:0.020706,(3:0.020605,(((((((4:0.025384,31:0.004815):0.001432,30:0.010339):0.058465,((((5:0,6:0.003537):0.043567,11:0.025338):0.011559,(((((((((9:0.005610,23:0.009319):0.004526,14:0.004721):0.001836,(24:0,25:0.010734):0.003278):0.004548,43:0.003677):0.001765,42:0.005587):0.002421,(10:0.011064,36:0.013072):0.010466):0.008299,39:0.028757):0.002633,(((16:0.012225,46:0.024470):0.056202,26:0.023052):0.004576,40:0.035226):0.001510):0.006604,(22:0.017888,(44:0.003963,45:0.005147):0.015952):0.003879):0.015475,((((32:0.004119,33:0.005941,35:0.003944):0.004065,37:0.001956):0.006002,38:0.001983):0.003885,34:0):0.024466):0.007447,(8:0.025792,(((17:0.007030,21:0.007402):0.001767,18:0.001732):0.001848,19:0.001722):0.026183):0.018764):0.013481):0.003337,(((12:0.063854,28:0.024140):0.057880,15:0.074856):0.109603,41:0.055561):0.018199):0.003477,7:0.023472):0.055157,(20:0.014635,27:0.019929):0.024485):0.060705,(13:0.005947,29:0.014261):0.103035):0.077798):0.017891); tree GAPDH_cons3 = [&U] (1,2,(3,(((((((4,(30,31)),7),(8,(17,((18,19),21))),11,(32,(33,37),(34,38),35)),((5,6),(((((((9,14),25),(10,23),24,(42,43)),39),36),26),((16,46),(22,(44,45))),40)),41),((12,28),15)),(20,27)),(13,29)))); [u] tree HMGN2_cons2 = [&U] (1,2,(3,(((((((4,(30,31)),7),(((32,35),(33,37)),(34,38))),(((5,6),11),(8,((17,21),18,19)))),((((((9,(((10,(14,36)),((23,25),24)),(42,43))),(16,46)),39,40),(22,(44,45))),26),41)),((12,28),15),(20,27)),(13,29)))); tree HSP90B1_cons2 = [&U] (1,2,(3,((((((((4,(30,31)),(7,((32,33,(35,37),38),34))),((5,6),11)),((8,((17,21),(18,19))),(((((((((9,23),(14,25)),(42,43)),(10,(24,36))),39),40),(16,46),26),(44,45)),22))),41),((12,28),15)),(20,27)),(13,29)))); [C] tree SERPIN [OVM] = [&U] (1:0.015214,2:0.016876,(3:0.028278,(((((((((4:0.008860,(30:0.002127,31:0.002130):0.007213):0.015963,7:0.024219):0.010699,(((5:0.003176,6:0.002103):0.021713,11:0.058672):0.013032,(8:0.033681,(17:0.006362,(18:0.001052,19:0.003155):0.003122,21:0):0.015258):0.010660):0.001123):0.002052,((((32:0.003143,33:0.001051):0.004191,35:0.002096,37:0.003154):0.004204,38:0.003183):0.001943,34:0.008610):0.027425):0.006180,(((((((9:0.005459,(10:0.011959,(42:0.009776,43:0.003227):0.004404):0.001058):0.001084,36:0.012070):0.000998,14:0.005404):0.002177,((23:0.001072,25:0.006470):0.001075,24:0.002151):0.001060):0.014338,39:0.035230):0.014496,(((16:0.006952,46:0.016902):0.018994,26:0.033894):0.000267,40:0.031177):0.005562):0.001030,(22:0.013186,(44:0.009845,45:0.006870):0.014026):0.010889):0.007500):0.000545,41:0.066688):0.011501,((12:0.027047,28:0.021494):0.014680,15:0.039067):0.032282):0.002446,(20:0.015064,27:0.011326):0.033555):0.045686,(13:0.017697,29:0.013700):0.051268):0.052190):0.009050); [u] tree OVM_cons2 = [&U] (1,2,(3,(((((4,(30,31)),((7,((12,28),15)),(8,((17,19,21),18)),(((((9,14,23,(24,25)),10,(42,43)),36),(44,45)),(16,46),(22,26),39,40))),((5,6),11),(((32,33,35,37),(34,38)),41)),(20,27)),(13,29)))); [C] tree RHO = [&U] (1:0.015435,2:0.019019,(3:0.031100,(((((((((4:0.003733,(30:0.002352,31:0.002362):0.013268):0.021249,((8:0.033445,((17:0.006192,18:0.006281,19:0.003698):0.001240,21:0.002501):0.017882):0.045275,(((32:0,(33:0,37:0.001207):0.002419):0.001083,35:0.004980):0.006277,(34:0.007451,38:0.009532):0.001313):0.035511):0.001267):0.004452,((5:0.003459,6:0.003575):0.041315,11:0.098178):0.022511):0.006032,7:0.028525):0.007149,((((((((9:0.011290,14:0.016278):0.001163,(((23:0.002454,24:0.008628):0.001195,25:0.012262):0.001263,36:0.023538):0.001240):0.002526,(42:0.013727,43:0.021262):0.005938):0.001128,10:0.008818):0.017953,39:0.039235):0.002081,((16:0.011688,46:0.011410):0.031411,40:0.030234):0.004404):0.002723,26:0.035952):0.004600,22:0.023196,(44:0.002390,45:0.002392):0.027103):0.041766):0.007619,41:0.114839):0.033309,((12:0.050949,28:0.033210):0.023994,15:0.049365):0.241088):0.012956,(20:0.021747,27:0.020699):0.065962):0.142839,(13:0.012676,29:0.018227):0.083514):0.150575):0.012419); End;