Jansen R.K. Ruck E.C. Nakov T. Ashworth M. Theriot E.C. Theriot E.C., Ashworth M., Nakov T., Ruck E.C., & Jansen R.K. 2016-07-01 Molecular Phylogenetics and Evolution Bremer support phylogenetic information profiling phylogenetic signal 3rd codon position chloroplast genes diatom phylogeny Dissecting signal and noise in diatom chloroplast protein encoding genes with phylogenetic information profiling Theriot E.C., Ashworth M., Nakov T., Ruck E.C., & Jansen R.K. 2015. Dissecting signal and noise in diatom chloroplast protein encoding genes with phylogenetic information profiling. Molecular Phylogenetics and Evolution, 89: 28-36. pythonVersion 2.7.9 pythonImplementation CPython Diatoms $1 ^(\S*\s+\S*).* false ^dc:contributor ^dc:creator ^dc:date ^dc:publisher ^dc:subject ^dc:title ^dcterms:bibliographicCitation ^ot:comment ^prism:creationDate ^prism:doi ^prism:endingPage ^prism:modificationDate ^prism:pageRange ^prism:publicationDate ^prism:publicationName ^prism:section ^prism:startingPage ^prism:volume ^skos:changeNote ^skos:historyNote ^tb:identifier.study ^tb:title.study @label ^skos:historyNote ^skos:prefLabel ^skos:prefLabel ^skos:prefLabel ^skos:prefLabel @label Tl2341709 Tl2341712 Tl2341713 Tl2341724 Tl2341730 Tl2341731 Tl2341736 Tl2341748 Tl2341749 Tl2341753 Tl2341756 Tl2341778 Tl2341781 Tl2341786 Tl2341788 Tl2341792 Tl2341794 Tl2341797 Tl2341799 Tl2341811 Tl2341818 Tl2341825 Tl2341829 Tl2341833 Tl2341848 Tl2341849 Tl2341850 Tl2341851 Tl2341867 Tl2341868 Tl2341872 Tl2341879 Tl2341886 Tl2341890 Tl2341911 Tl2341912 Tl2341915 Tl2341721 Tl2341754 Tl2341734 Tl2341744 Tl2341838 Tl2341735 Tl2341767 Tl2341740 Tl2341855 Tl2341746 Tl2341885 Tl2341758 Tl2341820 Tl2341760 Tl2341782 Tl2341816 Tl2341785 Tl2341888 Tl2341798 Tl2341895 Tl2341808 Tl2341908 Tl2341809 Tl2341870 Tl2341824 Tl2341905 Tl2341840 Tl2341907 Tl2341881 Tl2341902 ^skos:historyNote ^ot:isTaxonExemplar ^ot:isTaxonExemplar ^ot:isTaxonExemplar ^ot:isTaxonExemplar ^ot:isTaxonExemplar ^ot:isTaxonExemplar ^ot:isTaxonExemplar ^ot:isTaxonExemplar ^ot:isTaxonExemplar ^ot:isTaxonExemplar ^ot:isTaxonExemplar @label ^ot:isTaxonExemplar ^ot:isTaxonExemplar ^ot:isTaxonExemplar ^ot:isTaxonExemplar @label ^ot:isTaxonExemplar ^ot:isTaxonExemplar ^ot:isTaxonExemplar ^ot:isTaxonExemplar ^ot:isTaxonExemplar ^ot:isTaxonExemplar ^ot:isTaxonExemplar ^ot:isTaxonExemplar @label ^ot:isTaxonExemplar ^ot:isTaxonExemplar ^ot:isTaxonExemplar ^ot:isTaxonExemplar ^ot:isTaxonExemplar ^ot:branchLengthTimeUnit ^ot:nodeLabelMode ^ot:nodeLabelTimeUnit ^ot:reasonsToExcludeFromSynthesis ^tb:kind.tree ^tb:ntax.tree ^tb:quality.tree ^tb:type.tree ^ot:ottId Kaitlin Allen 6388659 Bacillariophyceae ot_1395 Theriot E.C., Ashworth M., Nakov T., Ruck E.C., & Jansen R.K. 2015. Dissecting signal and noise in diatom chloroplast protein encoding genes with phylogenetic information profiling. Molecular Phylogenetics and Evolution, 89: 28-36. 2015 2015-10-17 10.1016/j.ympev.2015.03.012 36 2016-07-01 28-36 2015 Molecular Phylogenetics and Evolution Study 28 89 Generated on Fri Jun 22 22:33:05 UTC 2018 Mapped from TreeBASE schema using org.cipres.treebase.domain.nexus.nexml.NexmlDocumentWriter@3901574c $Rev$ 18390 7 gene diatom phylogeny and phylogenetic information profiling Mapped from TreeBASE schema using org.cipres.treebase.domain.nexus.nexml.NexmlOTUWriter@32ea28a $Rev$ Surirella ovata HK214 801462 Surirella minuta Hyalodiscus sp CA HK344 Palmerina hardmaniana HK233 932699 Palmerina hardmaniana Diploneis subovalis HK084 625562 Diploneis subovalis Cocconeis sp. HK312 Tetracyclus sp. B16 Koernerella recticostata HK242 767865 Koernerella recticostata Stictocyclus stictodiscus HK269 4026123 Stictocyclus stictodiscus Neidium bisulcatum HK076 932704 Neidium bisulcatum Synedra ulna HK075 570317 Synedra ulna Bellerochea malleus HK265 613425 Bellerochea malleus Ardissonea formosa HK209 154604 Ardissonea formosa Chaetoceros peruvianus HK202 499052 Chaetoceros peruvianus Triceratium dubium CA_HK254 647156 Triceratium dubium Diatoma tenue HK078 621377 Diatoma tenue Bacillaria paxillifer HK130 446447 Bacillaria paxillifer Plagiogramma sp WA HK324 Achnanthes coarctata HK079 922019 Achnanthidium coarctatum Hyalodiscus stelliger HK042 867861 Podosira stelligera Podosira stelligera Coscinodiscus radiatus HK031 790047 Coscinodiscus radiatus Minidiscus trioculatus HK036 303302 Minidiscus trioculatus Rhizosolenia imbricata FL HK244 1024267 Rhizosolenia imbricata Eucampia sp HK260 Trieres sinensis HK037 Toxarium hennedyanum HK220 226480 Toxarium hennedyanum Cylindrotheca closterium HK180 1095886 Cylindrotheca closterium Cyclophora tenuis HK307 322451 Cyclophora tenuis Biddulphia tridens FL HK327 677903 Biddulphia tridens Actinocyclus sp GU52O HK347 Asterionellopsis socialis HK181 2818794 Asterionellopsis socialis Gyrosigma acuminatum HK085 52681 Gyrosigma acuminatum Scoliopleura peisonis HK103 750872 Scoliopleura peisonis Trieres mobiliensis HK204 134700 Odontella mobiliensis Lithodesmium undulatum HK029 1002046 Lithodesmium undulatum Melosira nummuloides HK041 1098707 Melosira nummuloides Neidium affine HK064 593705 Neidium affine Cyclophora tenuis HK216 322451 Cyclophora tenuis Bleakeleya notata HK247 365757 Bleakeleya notata Ardissonea fulgens v gigantea HK167 154588 Synedra fulgens Rhizosolenia formosa HK354 2811871 Rhizosolenia formosa Synedropsis cf recta HK110 Epipsammic chain FL HK316 Trieres regia HK322 2819379 Odontella regia Triceratium bicorne HK222 5358976 Triceratium bicorne Triceratium dictyotum HK281 2819270 Triceratium dictyotum Coscinodiscus sp Panama HK263 Triceratium dubium CanIsl HK342 647156 Triceratium dubium Odontella rhomboides HK282 2819510 Odontella rhomboides Mastogloia sp HK136 Staurosira construens HK071 433735 Fragilaria construens Lithodesmium intricatum CA HK231 712 Lithodesmium intricatum Cymatopleura elliptica HK215 371139 Cymatopleura elliptica Odontella aurita CanIsl HK333 1019315 Odontella aurita Rhabdonema arcuatum HK304 283903 Rhabdonema arcuatum Grammatophora oceanica HK147 92248 Grammatophora oceanica Lithodesmioides polymorpha HK211 717 Lithodesmioides polymorpha Amphipentas pentacrius HK289 4025718 Amphipentas pentacrius Cymatosira lorenziana HK283 2819576 Cymatosira lorenziana Aulacoseira granulata HK094 562857 Aulacoseira granulata Biddulphia tridens HK239 677903 Biddulphia tridens Terpsinoe musica HK273 556739 Terpsinoe musica Lemnicola hungarica HK129 573375 Lemnicola hungarica Aulacodiscus orientalis HK208 771549 Aulacodiscus orientalis Leyanella arenaria HK045 710597 Leyanella arenaria Gomphonema affine HK098 97396 Gomphonema affine Paralia sulcata HK048 987905 Paralia sulcata Stauroneis acuta HK059 750874 Stauroneis acuta Detonula confervacea HK111 332622 Detonula confervacea Berkeleya rutilans HK154 677899 Berkeleya rutilans (species in subkingdom SAR) Papiliocellulus simplex HK134 569605 Papiliocellulus simplex Proboscia sp FL HK300 Eucampia zodiacus TX HK320 791851 Eucampia zodiacus Fallacia monoculata HK082 52677 Fallacia monoculata Coscinodiscus sp FLconcave HK298 Odontella aurita HK203 1019315 Odontella aurita Rhizosolenia shrubsolei HK221 338628 Rhizosolenia shrubsolei Psammoneis japonica HK299 122870 Psammoneis japonica Odontella longicruris v hyalina HK284 812584 Odontella longicruris Actinoptychus sp HK050 Gomphonema parvulum HK081 1033662 Gomphonema parvulum Actinocyclus sp Panama HK262 Pinnularia brebissonii HK092 260775 Pinnularia brebissonii Asterionella formosa HK144 613419 Asterionella formosa Brockmanniella brockmannii HK040 1094149 Brockmanniella brockmannii Actinocyclus tinydrum CA HK346 Florella pascuensis HK175 699326 Florella pascuensis Plagiogrammopsis van heurckii HK293 Endictya oceanica HK259 4026128 Endictya oceanica Lampriscus orbiculatus HK125 573385 Lampriscus orbiculatum Tabularia cf tabulata HK109 Cerataulina pelagica HK232 103961 Cerataulina pelagica Triceratium sp HK047 Asterionellopsis glacialis HK107 230521 Asterionellopsis glacialis Corethron hystrix Corethron hystrix HK004 Pleurosira laevis HK068 959249 Pleurosira laevis Planktoniella sol HK035 1024261 Planktoniella sol Actinoptychus undulatus HK261 2812328 Actinoptychus undulatus Porosira glacialis HK115 601257 Porosira glacialis Tabellaria flocculosa HK065 79379 Tabellaria flocculosa Fragilariforma virescens HK132 570316 Fragilariforma virescens Biddulphia biddulphiana FL HK328 125309 Biddulphia biddulphiana Cerataulus smithii NC HK331 103957 Cerataulus smithii Podocystis spathulatum HK217 357098 Podocystis spathulata Nanofrustulum cf shiloi HK056 Centronella reicheltii HK150 677880 Centronella reicheltii Guinardia flaccida HK272 272514 Guinardia flaccida Ditylum brightwelli HK285 549288 Ditylum brightwellii Ditylum brightwellii Urosolenia eriensis HK054 647152 Urosolenia eriensis Odontella aurita Guam HK334 1019315 Odontella aurita Coscinodiscus wailesii HK229 897667 Coscinodiscus wailesii Stephanopyxis turris Stephanopyxis turris HK213 Bolidomonas pacifica Bolidomonas pacifica HK015 Lithodesmium intricatum HI HK253 712 Lithodesmium intricatum Ditylum sol HK240 2819304 Ditylum sol Amphora coffeaeformis HK089 827648 Amphora coffeiformis Navicula cryptocephala HK090 33945 Navicula cryptocephala Lampriscus shadboltianus v. crenulata HK257 573381 Lampriscus shadboltianum Opephora sp HK296 Minutocellus polymorphus HK043 303306 Minutocellus polymorphus Dimeregramma dubium Guam HK325 5426499 Dimeregramma dubium Trigonium formosum HK258 647165 Trigonium formosum Araphid ribbon FL HK315 Corethron hystrix FL HK241 Caloneis lewisii HK060 677907 Caloneis lewisii Attheya longicornis HK317 974720 Attheya longicornis Aualcodiscus oreganus HK348 Climaconeis riddleae HK178 103950 Climaconeis riddleae Extubocellulus cribriger HK046 595680 Extubocellulus cribriger Rhaphoneis amphiceros HK237 114508 Rhaphoneis amphiceros Craticula cuspidata HK061 148817 Craticula cuspidata Cyclophora tenuis HK308 322451 Cyclophora tenuis Synedra famelica HK072 277981 Fragilaria famelica Rhizosolenia setigera HK032 489192 Rhizosolenia setigera Tryblionella apiculata HK087 647166 Tryblionella apiculata Synedra bacillaris HK291 2819037 Synedra bacillaris Eunotia curvata HK086 671510 Eunotia bilunaris Leptocylindrus minimus Leptocylindrus minimus HK355 Guinardia delicatula HK205 272513 Guinardia delicatula Hemiaulus sinensis HK123 573393 Hemiaulus sinensis Staurosirella pinnata HK116 5987859 Staurosirella pinnata Actinocyclus sp FL HK345 Delphineis sp HK133 Diatoma elongatum Diatoma elongatum HK119 Eunotogramma sp HK294 Denticula kuetzingii HK104 625557 Denticula kuetzingii Ctenophora pulchella HK105 103966 Ctenophora pulchella Chaetoceros muelleri HK028 253195 Chaetoceros muellerii Chaetoceros muellerii Trieres mobiliensis HK227 134700 Odontella mobiliensis Odontella rostrata HK225 2819374 Odontella rostrata Cyclotella meneghiniana HK052 422808 Cyclotella meneghiniana Licmophora remulus HK302 646909 Licmophora remulus Amphitetras antediluviana HK223 154598 Amphitetras antediluviana Perideraion montgomeryii HK246 193672 Perideraion montgomeryi Phaeodactylum tricornutum HK011 529438 Phaeodactylum tricornutum Placoneis elginensis HK096 519424 Placoneis elginensis Licmophora paradoxa HK106 983609 Licmophora paradoxa Stellarima microtrias HK108 741174 Stellarima microtrias Cocconeis placentula HK077 148815 Cocconeis placentula Biddulphia sculpta HK252 2819489 Biddulphia sculpta Proboscia sp TX HK236 Pseudosolenia calcaravis HK245 Neidium productum HK063 932702 Neidium productum Cerataulus smithii TX HK224 103957 Cerataulus smithii Acanthoceras zachariasii HK250 2812609 Acanthoceras zachariasii Dactylosolien blavyanus HK301 Synedropsis hyperborea HK117 427003 Synedropsis hyperboreoides Synedropsis hyperboreoides Campylosira cymbelliformis HK122 677909 Campylosira cymbelliformis Hyalosira interrupta HK248 73218 Hyalosira interrupta Chrysanthemodiscus floriatus HK171 2812375 Chrysanthemodiscus floriatus Toxarium undulatum HK210 1010309 Toxarium undulatum Eunotia glacialis HK069 52675 Eunotia glacialis Achnanthes sp. HK311 Roundia cardiophora HK219 2811603 Roundia cardiophora Striatella unipunctata HK177 433732 Striatella unipunctata Ellerbeckia arenaria B12 2812012 Ellerbeckia arenaria Biddulphiopsis membranacea HK166 677901 Biddulphiopsis membranacea Meuneira membranacea HK313 2816666 Meuniera membranacea Ardissonea fulgens HK305 154588 Synedra fulgens Achnanthes sp. HK303 Plagiogramma staurophorum HK212 932710 Plagiogramma staurophorum Odontella longicruris HK226 812584 Odontella longicruris Cyclostephanos dubius HK051 625560 Cyclostephanos dubius Cyclotella sp HK126 Arcocellulus mammifer HK044 534572 Arcocellulus mammifer Cyclophora castracanei HK243 594688 Cyclophora castracanei Corethron sp OR HKXXX Coscinodiscus concinnus HK267 103952 Coscinodiscus concinnus Cerataulina pelagica HK230 103961 Cerataulina pelagica Thalassiosira pseudonana HK008 753596 Thalassiosira pseudonana Cyclophora tabellariformis HK306 594696 Cyclophora tabellariformis Mastodiscus radiatus HK249 427532 Mastodiscus radiatus Eunotia pectinalis HK153 663774 Eunotia pectinalis Nitzschia filiformis HK073 671507 Nitzschia filiformis Melosira varians HK266 28082 Melosira varians Striatella unipunctata FL HK318 433732 Striatella unipunctata Actinocyclus subtilis HK168 2812103 Actinocyclus subtilis Leptocylindrus danicus TX HK238 Lampriscus shadboltianus HK264 573381 Lampriscus shadboltianum Bellerochea horologicalis HK235 154594 Bellerochea horologicalis Rhizosolenia setigera TX HK268 489192 Rhizosolenia setigera Biddulphia biddulphiana HK271 125309 Biddulphia biddulphiana Biddulphia alternans HK292 677897 Biddulphia alternans Amphipleura pellucida HK287 2816804 Amphipleura pellucida Dimeregramma sp TX HK288 Entomoneis sp. Entomoneis sp. HK135 Attheya septentrionalis HK112 312518 Attheya septentrionalis Fallacia pygmaea HK093 52679 Fallacia pygmaea Pinnularia terminata HK088 Mapped from TreeBASE schema using org.cipres.treebase.domain.nexus.nexml.NexmlTreeBlockWriter@3defb653 $Rev$ ot:changesCount Maximum likelihood Tn14187433 Tn14187433 false Species Tree 202 Unrated Single true true true true true true true true true true true true true true true true true true true true true true true true true true true true true true true true true true true true true true true true true true false true true true false true true true true true true true true true false true true true true true true true true true true true true true true true true true true true true true true true false true true true true true true true true false true true true false true true false true true true true true false true true true true true true false true true true true false true true true true true true true true true true true true true true true false true true true true true true true false true true true true true false true true true true true true true true true true true true true true true true true true true true true true true true true true true true true true true true true true true true true true true false true true true false true true true true true true true true true true true true true true true true true true true true true true true true true true true true true true true true true true true true true true true true true