Title Time for a rethink: time sub-sampling methods in disparity- through-time analyses Authors Guillerme, T; Cooper, N Date Submitted 2018-04-24 Supporting Information: S1 Guillerme & Cooper 2018 Supporting Information from “Time for a rethink: time sub-sampling methods in disparity-through-time analyses” APPENDIX S1: ADDITIONAL DETAILS OF DATASETS Beck2014 (Figure A1) The following taxa were removed because they were in the phylogeny but not the character matrix or vice versa: Montanalestes, Lainodon, Kharmerun- gulatum, Alymlestes. Brusatte2014 (Figure A2) We used one randomly selected time-scaled tree from Brusatte et al. (2014). Zero-length branches were replaced with the minimum branch length in the phylogeny. The following taxa were removed because they were in the phylogeny but not the character matrix or vice versa: Sinraptor dongi, Hesperonychus elizabethae, Pyroraptor olympius, Limenavis patagonica, Lithornis, Crypturellus undulatus, Gallus gallus, Crax pauxi, Anas platyrhynchus, Chauna torquata, Epidendrosaurus and Kinnareemimus. The following taxa were removed because they shared no characters in the morphological matrix: Shanag ashile, Atrociraptor marshalli, Proceratosaurus bradleyi, Incisivosaurus gauthieri, Enigmosaurus, Nanshiungosaurus brevispi- nus, Xixiasaurus, Tsaagan mangas, Mirischia, Pedopenna, Suzhousaurus, Ju- ratyrant, Vorona, Bonapartenykus, Teratophoneus, Gobipteryx, Songlingornis, Liaoningornis longidigitu and Achillesaurus. Bapst2016 (Figure A3) We used the maximum clade credibility tree from Bapst et al. (2016). Zero-length branches were replaced with the minimum branch length in the phylogeny. The following taxa were removed because they were in the phylogeny but not the character matrix or vice versa: Mei long and Mei lon. The following taxa were removed because they shared no characters in the morphological matrix: Hagryphus giganteus, Atrociraptor marshalli, IGM100 1015 UndesDromaeosaurid, Dromaeosaurus albertensis, Incisivosaurus gauthieri, Deinocheirus mirificus, Therizinosaurus cheloniformis, Anserimimus planinychus and Elmisaurus rarus. Supporting Information: S1 Guillerme & Cooper 2018 Wright2017 (Figure A4) We used the maximum clade credibility tree from Wright (2017). To prop- erly timescale the tree we followed the advice of Wright (2017) and di- vided the branch lengths by the corresponding clock rate (= 0.03517385) and then set the root time to 485.4. Zero-length branches were replaced with the minimum branch length in the phylogeny. No taxa were re- moved. Simpsonotus Thomashuxleya Pyrotherium Henricosbornia Trigonostylops Diadiaphorus Hyracotherium Periptychus Mioclaenus Paulacoutoia Didolodus Chriacus Arctocyon Phenacodus Meniscotherium Hyopsodus Diacodexis Gujaratia Eoryctes Solenodon Erinaceus Soricidae Icaronycteris Miacis Vulpavus Protictis Patriomanis Adapis Notharctus Plesiadapis Purgatorius Cynocephalus Ptilocercus Mimotona Gomphos Rhombomylus Paramys Tribosphenomys Trichechus Pezosiren Moeritherium Procavia Rhynchocyon Orycteropus Widanelfarasia Dilambdogale Microgale Potamogalinae Todralestes Myrmecophagidae Bradypus Dasypodidae Oxyprimus Protungulatum Oxyclaenus Leptictis Gypsonictops Barunlestes Zalambdalestes unnamed zalambdalestid Zhangolestes Kulbeckia Batodon Maelestes unnamed cimolestid Cimolestes Ukhaatherium Asioryctes Kennalestes Uchkudukodon Bulaklestes Daulestes Afrodon chleuhi Afrodon germanicus Deccanolestes cf hislopi Deccanolestes hislopi Deccanolestes narmadensis Deccanolestes robustus Zhelestes Aspanlestes Eoungulatum Parazhelestes Avitotherium Alostera Gallolestes Eozhelestes Sheikhdzheilia Borisodon Paranyctoides Bobolestes Murtoilestes Prokennalestes Eomaia Pucadelphys Mayulestes Deltatheridium Kielantherium Acristatherium Juramaia Vincelestes Peramus Nanolestes Upper Albian Aptian Middle Danian Lutetian Chattian Toarcian Turonian Bajocian Aalenian Ypresian Rupelian Gelasian Callovian Tithonian Langhian Zanclean Tortonian Calabrian Oxfordian Bartonian Coniacian Selandian Thanetian Messinian Bathonian Santonian Berriasian Barremian Aquitanian Priabonian Piacenzian Burdigalian Hauterivian Campanian Valanginian Serravallian Cenomanian Maastrichtian Kimmeridgian Lower Lower Upper Upper Middle Eocene Miocene Pliocene Holocene Oligocene Paleocene Pleistocene Jurassic Cretaceous Paleogene Neogene Quat. 0 90 80 70 60 50 40 30 20 10 180 170 160 150 140 130 120 110 100 Figure A1: Phylogeny from Beck & Lee (2014). Supporting Information: S1 Guillerme & Cooper 2018 Allosaurus fragilis Bicentenaria Zuolong Tanycolagreus Coelurus fragilis Dilong paradoxus Kileskus Sinotyrannus Guanlong Eotyrannus lengi Xiongguanlong Dryptosaurus Appalachiosaurus Bistahieversor Gorgosaurus libratus Albertosaurus sacrophagus Alioramus Daspletosaurus Tarbosaurus baatar Tyrannosaurus rex Tugulusaurus Ornitholestes hermanni Juravenator starki Sinosauropteryx prima Compsognathus longipes Sinocalliopteryx Huaxiagnathus orientalis Nqwebasaurus Pelecanimimus polydon Shenzhousaurus orientalis Beishanlong Harpymimus okladnikovi Garudimimus brevipes Sinornithomimus Archaeornithomimus asiati Gallimimus bullatus Anserimimus planinychus Qiupalong Struthiomimus altus Ornithomimus edmonticus Falcarius Beipiaosaurus Alxasaurus elesitaiensis Erliansaurus Neimongosaurus Therizinosaurus Erlikosaurus andrewsi Nothronychus Segnosaurus galbinensis Haplocheirus Alvarezsaurus calvoi Patagonykus puertai Albertonykus Xixianykus Albinykus Ceratonykus Mononykus olecranus Shuvuuia deserti Linhenykus Parvicursor Epidexipteryx Caudipteryx zoui Avimimus portentosus Microvenator celer Chirostenotes pergracilis Citipati osmolskae Conchoraptor gracilis Ingenia yanshani Rinchenia mongoliensis Oviraptor philoceratops Mahakala omnogovae Rahonavis ostromi Buitreraptor gonzalozorum Austroraptor Neuquenraptor plus Unenlagia Graciliraptor lujiatunensis Tianyuraptor ostromi Sinornithosaurus millenii Microraptor zhaoianus Achillobator giganticus Utahraptor Dromaeosaurus albertensis Saurornitholestes langsto Bambiraptor feinbergorum Deinonychus antirrhopus Adasaurus mongoliensis Balaur bondoc Velociraptor mongoliensis Anchiornis huxleyi Eosinopteryx Aurornis Xiaotingia IGM 100 slash 1323 IGM 100 slash 1126 Jinfengopteryx elegans Mei long Sinovenator changii EK troodontid IGM 100 slash 44 Byronosaurus jaffei Sinornithoides youngi Troodon formosus Zanabazar junior Saurornithoides mongolien Archaeopteryx lithographi Sapeornis Jeholornis prima Jixiangornis orientalis Confuciusornis sanctus Pengornis houi Neuquenornis volans Concornis Cathayornis Patagopteryx deferrariisi Hongshanornis longicrest Yanornis martini Yixianornis Apsaravis ukhaana Iaceornis marshii Ichthyornis Baptornis Hesperornis Albian Aptian Danian Lutetian Toarcian Turonian Bajocian Aalenian Ypresian Callovian Tithonian Oxfordian Bartonian Coniacian Selandian Thanetian Bathonian Santonian Berriasian Barremian Hauterivian Campanian Valanginian Cenomanian Maastrichtian Kimmeridgian Lower Lower Upper Upper Middle Eocene Paleocene Jurassic Cretaceous Paleogene 90 80 70 60 50 40 170 160 150 140 130 120 110 100 Figure A2: Phylogeny from Brusatte et al. (2014). This is one randomly selected tree from the time-scaled trees in the paper. Supporting Information: S1 Guillerme & Cooper 2018 Haplocherius Compsognathus longipes Sinosauropteryx prima Huaxiagnathus orientalis Harpymimus okladnikovi Shenzhousaurus orientalis Garudimimus brevipes Gallimimus bullatus Struthiomimus altus Ornithomimus edmontonicus Archaeornithomimus asiaticus Pelecanimimus polyodon Alvarezsaurus calvoi Shuvuuia deserti Mononykus olecranus Patagonykus puertai Xiaotingia zhengi Anchiornis huxleyi Yanornis martini Protopteryx fengningensis Confuciusornis sanctus Sapeornis chaoyangensis Jeholornis prima Wellnhoferia grandis Archaeopteryx lithographica NGMC91 UnnamedDromaeosaurid Microraptor zhaoianus Sinornithosaurus millenii Utahraptor ostrommaysi Achillobator giganticus Deinonychus antirrhopus Saurornitholestes langstoni Velociraptor mongoliensis Adasaurus mongoliensis Bambiraptor feinbergi Buitreraptor gonzalezorum Rahonavis ostromi Unenlagia Sinovenator changii Zanabazar junior Saurornithoides mongoliensis Troodon formosus IGM100 44 unnamedtroodontid Sinornithoides youngi Byronosaurus jaffei Epidexipteryx ningchengensis Epidendrosaurus ningchengensis Similicaudipteryx Caudipteryx Microvenator celer Avimimus portentosus Oviraptor philoceratops Conchoraptor gracilis Khaan mckennai Heyuannia huangi Ingenia yanshini Citipati osmolskae IGM100 42 UnnamedOviraptorid Rinchenia mongoliensis Chirostenotes pergracilis Protarchaeopteryx robusta Neimongosaurus yangi Segnosaurus galbiensis Erlikosaurus andrewsi Nanshiungosaurus brevispinus Erliansaurus bellamanus Nothronychus mckinleyi Alxasaurus elesitaiensis Beipiaosaurus inexpectus Falcarius utahensis Ornitholestes hermanni Coelurus fragilis Tanycolagreus topwilsoni Gorgosaurus libratus Tyrannosaurus rex Eotyrannus lengi Dilong paradoxus Sinraptor Allosaurus fragilis Albian Aptian Norian Danian Lutetian Toarcian Turonian Bajocian Aalenian Ypresian Rupelian Rhaetian Callovian Tithonian Oxfordian Bartonian Coniacian Selandian Thanetian Bathonian Santonian Berriasian Barremian Priabonian Hettangian Sinemurian Hauterivian Campanian Valanginian Cenomanian Maastrichtian Kimmeridgian Pliensbachian Lower Lower Upper Upper Upper Middle Eocene Oligocene Paleocene Triassic Jurassic Cretaceous Paleogene 90 80 70 60 50 40 210 200 190 180 170 160 150 140 130 120 110 100 Figure A3: Phylogeny from Bapst et al. (2016). This is the maximum clade credibility tree. Supporting