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BM CC EB What Can We Learn from a Tree? Leaf N Ca Introduction to Comparative Methods BM CC EB What can we learn from a tree? Leaf N Ca Co r y SLA op r nales h yllales Max height icales r Berbe oliales f Leaf size E Santalales r Aqui idopsidales Escalloniaceae ales Seed mass r Aste runiales B yphiaceae Apiales r rac Malpighiales a Eric. P ales Dipsacalesry Icacinaceaeaginaceae Gar r Bo Cary. Gentianales Oxalidales Solanales Celast Ast. rales Cucurbitales Ast2. Fagales Lamiales Rosales Fab. Fabales Monilophyte yllales Bras. Zygoph Gymn. Rosid. Cycadales Brassicales Gnetales Magn. Pinales Nymphaeales Arec. Austrobail Chlo vales Mono. Canellalesranthaceaeey Mal Pipe ales rales rteales Lau r Hue Myrt. ales Magnoliales P andanales Sapindales Dioscoreales Commelinales Prot. Zingibe Arecacales rales rtales Crossosomatales My P oales aniales r Vitales Ge agales r ales r Aspa s Saxif e l Buxaceae Proteales a r Dilleniaceae i Gunne agales aceae l i r Sabiaceae L unculales n Aco Ra Alismatales Cornwell et al. 2014 J Ecology making trees is hard.... because trees are information-rich the coming age of the megaphylogeny* * trees that are too big for your brain ensembl Why do you want to make or use trees? What do you hope to learn? What can you do? • Diversification (speciation and extinction) • Character evolution • Characters and diversification • Biogeography • Testing complex evolutionary models Diversification (speciation and extinction) Sharks Polypteriformes Chondrostei Amiiformes Elopomorpha Osteoglossomorpha Ostariophysi Clupeomorpha Esociformes Salmoniformes Galaxiiformes Stomiiformes Osmeriformes Argentiniformes Aulopiformes Myctophiformes Beryciformes+Stephanoberyciformes Ophidiiformes Percomorpha Scombridae Polymixiiformes Lampriformes Percopsiformes Zeiforms Latimeridae Dipnoi Gymnophiona Anura Caudata Monotremes Marsupials Boreoeutheria Afrotheria+Xenarthra Sphenodon NongekkoSquamates Taxa Gekkos 1 Pleurodira 5 Cryptodira Crocodylinae 10 Gavialidae 50 Camininae 100 Alligatorinae 500 Tinamiformes 1000 Struthioniformes 5000 Neoaves 10000 Galliformes 20000 Anseriformes 500 400 300 200 100 0 MYA Character evolution ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● Siren intermedia Siren lacertina Pseudobranchus striatus Pseudobranchus axanthus Onychodactylus fischeri Ranodon sibiricus Paradactylodon mustersi Paradactylodon gorganensis shift direction Pachyhynobius shangchengensis Hynobius formosanus Hynobius sonani Hynobius retardatus Hynobius boulengeri Hynobius kimurae Hynobius abei Hynobius lichenatus Hynobius tokyoensis 1.00 Hynobius nigrescens Hynobius takedai Hynobius stejnegeri Hynobius katoi Hynobius chinensis Hynobius yiwuensis Hynobius amjiensis Hynobius guabangshanensis Hynobius leechii 0.80 Hynobius okiensis Hynobius tsuensis Hynobius dunni Hynobius nebulosus Hynobius hidamontanus Salamandrella keyserlingii Liua tsinpaensis Liua shihi 0.50 Batrachuperus yenyuanensis Batrachuperus tibetanus Batrachuperus pinchonii Batrachuperus londongensis Cryptobranchus alleganiensis Andrias japonicus Andrias davidianus Necturus punctatus Necturus maculosus 0.20 Necturus lewisi Necturus beyeri Necturus alabamensis Proteus anguinus Rhyacotriton variegatus Rhyacotriton cascadae Rhyacotriton kezeri Rhyacotriton olympicus 0.00 Amphiuma tridactylum Amphiuma means Amphiuma pholeter Desmognathus auriculatus Desmognathus brimleyorum Desmognathus monticola Desmognathus fuscus Desmognathus welteri Desmognathus ochrophaeus point.seq -0.20 Desmognathus imitator Desmognathus marmoratus Desmognathus quadramaculatus Desmognathus aeneus Desmognathus wrighti Phaeognathus hubrichti Aneides flavipunctatus Aneides ferreus -0.50 Aneides lugubris Aneides hardii Aneides aeneus Ensatina eschscholtzii Hydromantes platycephalus Hydromantes italicus Karsenia koreana Plethodon albagula Plethodon glutinosus -0.80 Plethodon cylindraceus Plethodon teyahalee Plethodon cheoah Plethodon shermani Plethodon meridianus Plethodon amplus Plethodon montanus Plethodon ouachitae -1.00 Plethodon caddoensis Plethodon jordani Plethodon metcalfi Plethodon kentucki Plethodon yonahlossee Plethodon dorsalis Plethodon ventralis Plethodon angusticlavius Plethodon welleri Plethodon punctatus Plethodon wehrlei Plethodon hubrichti Plethodon nettingi Plethodon richmondi Plethodon shenandoah Plethodon cinereus Plethodon hoffmani Plethodon serratus Plethodon idahoensis Plethodon vandykei Plethodon neomexicanus Plethodon dunni Plethodon vehiculum Plethodon elongatus Eurycea tridentifera Eurycea neotenes Eurycea sosorum Eurycea nana Eurycea rathbuni Eurycea wilderae Bolitoglossinae Eurycea junaluska Eurycea bislineata Eurycea cirrigera Eurycea longicauda Eurycea lucifuga Eurycea quadridigitata Eurycea spelaea Eurycea tynerensis Eurycea multiplicata Pseudotriton ruber Pseudotriton montanus Gyrinophilus porphyriticus Stereochilus marginatus Batrachoseps major Batrachoseps attenuatus posterior rates Batrachoseps wrightorum Cryptotriton nasalis Cryptotriton alvarezdeltoroi Nyctanolis pernix Dendrotriton rabbi Dendrotriton cuchumatanus rep(-0.5, length(point.seq)) Nototriton barbouri Nototriton richardi Nototriton guanacaste 3.011 Nototriton picadoi Nototriton abscondens Oedipina uniformis Oedipina pacificensis Oedipina poelzi Oedipina pseudouniformis Oedipina cyclocauda Oedipina gephyra Oedipina elongata 0.519 Oedipina parvipes Oedipina complex Oedipina savagei Bradytriton silus Thorius troglodytes Thorius dubitus Chiropterotriton magnipes Chiropterotriton chondrostega 0.090 Chiropterotriton multidentatus Chiropterotriton priscus Chiropterotriton lavae Chiropterotriton dimidiatus Chiropterotriton arboreus Pseudoeurycea scandens Pseudoeurycea galeanae Pseudoeurycea cephalica Pseudoeurycea naucampatepetl 0.015 Pseudoeurycea gigantea Pseudoeurycea boneti Pseudoeurycea bellii Pseudoeurycea goebeli Pseudoeurycea brunnata Pseudoeurycea exspectata Pseudoeurycea rex Pseudoeurycea smithi 0.003 Pseudoeurycea anitae Pseudoeurycea cochranae Pseudoeurycea gadovii Pseudoeurycea melanomolga Pseudoeurycea longicauda Pseudoeurycea robertsi Pseudoeurycea altamontana Pseudoeurycea unguidentis Pseudoeurycea saltator point.seq 0.000 Pseudoeurycea juarezi Pseudoeurycea werleri Pseudoeurycea mystax Pseudoeurycea nigromaculata Pseudoeurycea lynchi Pseudoeurycea leprosa Pseudoeurycea firscheini Lineatriton lineolus 0.000 Parvimolge townsendi Ixalotriton parvus Ixalotriton niger Bolitoglossa hartwegi Bolitoglossa rufescens Bolitoglossa occidentalis Bolitoglossa odonnelli Bolitoglossa lignicolor Bolitoglossa yucatana 0.000 Bolitoglossa striatula Bolitoglossa mexicana Bolitoglossa platydactyla Bolitoglossa flaviventris Bolitoglossa macrinii Bolitoglossa riletti Bolitoglossa hermosa Bolitoglossa rostrata 0.000 Bolitoglossa helmrichi Bolitoglossa engelhardti Bolitoglossa lincolni Bolitoglossa franklini Bolitoglossa porrasorum Bolitoglossa longissima Bolitoglossa decora Bolitoglossa synoria Bolitoglossa celaque Bolitoglossa morio Bolitoglossa dunni Bolitoglossa diaphora Bolitoglossa conanti Bolitoglossa carri Bolitoglossa dofleini Bolitoglossa subpalmata Bolitoglossa pesrubra Bolitoglossa gracilis Bolitoglossa marmorea Bolitoglossa minutula Bolitoglossa cerroensis Bolitoglossa schizodactyla Bolitoglossa colonnea Bolitoglossa sima Bolitoglossa biseriata Bolitoglossa palmata Bolitoglossa peruviana Bolitoglossa altamazonica Bolitoglossa medemi Bolitoglossa adspersa Hemidactylium scutatum Pleurodeles waltl Pleurodeles poireti Tylototriton vietnamensis Tylototriton hainanensis Tylototriton asperrimus Tylototriton wenxianensis Tylototriton kweichowensis Tylototriton verrucosus Tylototriton taliangensis Echinotriton andersoni Echinotriton chinhaiensis Pachytriton brevipes Pachytriton labiatus Paramesotriton deloustali shift probability Paramesotriton fuzhongensis Paramesotriton guangxiensis Paramesotriton hongkongensis Paramesotriton chinensis Paramesotriton caudopunctatus Paramesotriton laoensis rep(-0.5, length(point.seq)) Cynops ensicauda Cynops pyrrhogaster Cynops cyanurus 1.000 Cynops chenggongensis Cynops orphicus Cynops orientalis Neurergus strauchii Neurergus microspilotus Neurergus kaiseri Neurergus crocatus Ommatotriton vittatus Ommatotriton ophryticus 0.875 Calotriton asper Calotriton arnoldi Triturus carnifex Triturus dobrogicus Triturus karelinii Triturus cristatus Triturus marmoratus Triturus pygmaeus 0.750 Lissotriton boscai Lissotriton italicus Lissotriton helveticus Lissotriton montandoni Lissotriton vulgaris Mesotriton alpestris Euproctus platycephalus Euproctus montanus Notophthalmus viridescens 0.625 Notophthalmus perstriatus Notophthalmus meridionalis Taricha rivularis Taricha sierrae Taricha torosa Taricha granulosa Mertensiella caucasica Chioglossa lusitanica 0.500 Lyciasalamandra atifi Lyciasalamandra helverseni Lyciasalamandra antalyana Lyciasalamandra billae Lyciasalamandra fazilae Lyciasalamandra luschani Lyciasalamandra flavimembris Salamandra salamandra Salamandra atra point.seq 0.375 Salamandra corsica Salamandra lanzai Salamandra infraimmaculata Salamandra algira Salamandrina perspicillata Salamandrina terdigitata Ambystoma gracile Ambystoma maculatum 0.250 Ambystoma macrodactylum Ambystoma californiense Ambystoma rosaceum Ambystoma dumerilii Ambystoma rivulare Ambystoma lermaense Ambystoma granulosum Ambystoma altamirani Ambystoma velasci 0.125 Ambystoma taylori Ambystoma tigrinum Ambystoma ordinarium Ambystoma andersoni Ambystoma flavipiperatum Ambystoma mexicanum Ambystoma amblycephalum Ambystoma jeffersonianum 0.000 Ambystoma laterale Ambystoma annulatum Ambystoma cingulatum Ambystoma bishopi Ambystoma opacum Ambystoma barbouri Ambystoma texanum Dicamptodon aterrimus Dicamptodon ensatus Dicamptodon tenebrosus Dicamptodon copei photos from wiki commons Characters and diversification Silvestro et al. 2013 Evolution Biogeography Ree and Smith 2008 Sys Biol Testing Complex Evolutionary Models Price et al. 2014 Nature.
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