RaiaCopesRule: Dated Trees and Trait Data for Ammonites, Ceratopsians and...

In dwbapst/paleotree: Paleontological and Phylogenetic Analyses of Evolution

Dated Trees and Trait Data for Ammonites, Ceratopsians and Cervids from Raia et al. 2015

Description

Dated phylogenetic trees for fossil ammonite genera, fossil ceratopsian species and (both extinct and extant) cervid species, as well as trait data (shell diameter and fractal complexity of the first suture) for the ammonite dataset, taken from the recent publication by Raia et al. (2015) in The American Naturalist. The goal of this paper was to examine the relationship between ornamental complexity and body size in three very different groups, but the datasets are very relatively large and useful for demonstrating application of comparative methods to fossil trees.

Format

The attached datasets consist of three phylogenetic trees as phylo objects, a data.frame consisting of three traits for ammonites (the third trait is the log of stratigraphic duration), and the two physical traits (shell size and suture complexity) as separate vectors, with taxon names.

Details

It appears that the trees were dated with tips at the last appearances, although this doesn't appear to be explicitly stated in Raia et al.

Source

These datasets were taken from the following study: Raia, P., F. Passaro, F. Carotenuto, L. Maiorino, P. Piras, L. Teresi, S. Meiri, Y. Itescu, M. Novosolov, M. A. Baiano, R. Martinez, and M. Fortelius. 2015. Cope's Rule and the Universal Scaling Law of Ornament Complexity. The American Naturalist. 186(2):165-175.

And the corresponding Dryad repository: Raia P, Passaro F, Carotenuto F, Maiorino L, Piras P, Teresi L, Meiri S, Itescu Y, Novosolov M, Baiano MA, Martinez R, Fortelius M (2015) Data from: Cope's rule and the universal scaling law of ornament complexity. Dryad Digital Repository. (doi: 10.5061/dryad.50dr8)

See Also

retiolitinae, macroperforateForam

Examples

data(RaiaCopesRule)

# plotting trees
plot(ladderize(ammoniteTreeRaia));axisPhylo()

plot(ceratopsianTreeRaia);axisPhylo()

plot(cervidTreeRaia);axisPhylo()

# plotting traitgrams for ammonites
plotTraitgram(tree = multi2di(ammoniteTreeRaia), trait = sutureComplexity,
	 conf.int = FALSE, main = "Ammonite Suture Complexity")

plotTraitgram(tree = multi2di(ammoniteTreeRaia), trait = shellSize,
	 conf.int = FALSE, main = "Ammonite Shell Diameter")

##############################################################################################

# The data set was generated by sourcing the following script:
	 


library(paleotree)

# Let's read in the trees from Raia et al 2015, AmNat
	# following is taken from their supplemental appendix, available at AmNat
# they all appear to be trees dated to the last appearance times
	# *and* specifically the end-boundary of the interval containing the last appearance

#########################################
# ammonite genera

ammoniteTreeRaia <- paste0("(((((Araxoceras:4,Eoaraxoceras:4)Araxoceratidae:26.5,Pseudasp",
 "idites:33.199997,Dieneroceras:37.300003,(Tardicolumbites:13.000015,Cowboyiceras:13.000023)",
 "Dinaritaceae:24.299988,Grambergia:42.5,(Amphipopanoceras:6, Megaphyllites:46.399994)Megaph",
 "yllitaceae:36.5,(Proteusites:11,Nathorstites:21)Nathorstitaceae:31.5,(Inyoites:7,Lanceolit",
 "es:7,Parussuria:7)Noritaceae:30.300003,(((Placites:66.700012,((Acrochordiceras:10.199997, ",
 "Bradyia:10.199997,Globacrochordiceras:5,Paracrochordiceras:10.199997)Acrochordiceratidae:9",
 ".000015,Balatonites:19.200012,(Favreticeras:10,Guexites:10,Gymnotoceras:10)Beyrichitidae:9",
 ".200012, Eogymnotoceras:19.200012,Goricanites:14.000015)Ceratitaceae:7.100006)clade_16:7.0",
 "99976, (((Gaudemerites:13.000015,(Owenites:9.000015,Prosphingites:9.000015)Paranannitidae:",
 "4,Meekoceras:13.000015, Arctoceras:13.000015)Meekoceratoidea:5.06665,(((Riedelites:85.6000",
 "06,((((Berriasella:15.399994, (Polyptychites:20.399994,Surites:14)Polyptychitidae:1.399994",
 ")clade_32:1.400002,Bodrakiceras:20.300003, Busnardoites:16.800003,Campylotoxia:20.300003,K",
 "arakaschiceras:23.199997,Luppovella:16.800003,Malbosiceras:13, Pomeliceras:13.399994)Neoco",
 "mitidae:21.199997,(Otohoplites:8.199997,Sonneratia:4.5,Anadesmoceras:4.5, Anahoplites:20,A",
 "rcthoplites:8.199997,Cleoniceras:8.199997,Dimorphoplites:8.199997,Epihoplites:20, Gastropl",
 "ites:13.900002,Grycia:13.900002,Hoplites:13.900002)Hoplitidae:60.899994)clade_29:20.200005",
 ", (Engonoceras:20.400002,(Knemiceras:16.400002,Parengonoceras:7,Platiknemiceras:7)Knemicer",
 "atidae:4) Engonoceratoidea:74.600006,(((Glochiceras:11,(Aconeceras:36.799995,Falciferella:3",
 "5.899994,Protaconeceras:7, Sanmartinoceras:24.369995)Oppeliidae:25.400009)Haplocerataceae:",
 "15.775009,(((Mortoniceras:16.300003, Oxytropidoceras:14)Brancoceratidae:27.633331,((Parado",
 "lphia:12.700005,Stoliczkaia:18.800003,Tegoceras:7) Lyelliceratidae:7.566666,((Borissiakoce",
 "ras:10.5,Mammites:7,Mantelliceras:12.800003)Acanthoceratidae:11.783333, (Neoptychites:6,Va",
 "scoceras:6)Vascoceratidae:12.783333)clade_49:11.783333)clade_47:7.566666)clade_45:7.566666",
 ", (Epileymeriella:5,Leymeriella:11.099998)Leymeriellidae:30.400002,(Beudanticeras:44.03332",
 "5, Burckhardtites:21.303329,(Barremites:1.666672,Desmoceras:48.166672)clade_55:1.666656, P",
 "seudohaploceras:21.303329,Pseudosaynella:21.303329,Pseudosilesites:21.303329,(Puzosia:56.6",
 "50002, (Forbesiceras:27.666664,(Melchiorites:6.083328,Uhligella:15.48333)clade_58:6.083336",
 ")clade_57:6.083336) clade_56:6.083328,Valdedorsella:33.633331,Zuercherella:33.73333)Desmoc",
 "eratidae:1.666667) Acanthocerataceae:42.575012)clade_39:15.774994,((Coroniceras:1.25,(Mega",
 "tyloceras:76.203336, (Zugodactylites:10.016663,Amaltheus:2.616669)Eoderocerataceae:2.61666",
 "9)clade_61:2.616669)clade_60:1.25, Oxynoticeras:9.100006)Psilocerataceae:1.25)clade_38:1.2",
 "5)Ammonitina:4,((Saghalinites:14,Tetragonites:14) Tetragonitidae:22,(Eogaudryceras:4,Gaudr",
 "yceras:32,Zelandites:32)Gaudryceratidae:4)Tetragonitoidea:97.100006, (Costidiscus:12.00000",
 "8,Macroscaphites:34.860008)Macroscaphitidae:64.139999)Ammonitida:30.222214, (Ammonitoceras",
 ":98.570007,Argonauticeras:98.570007,Audaxlytoceras:27.600006,Holcolytoceras:21, (Eulytocer",
 "as:65.713333,Jaubertella:78.043335)clade_84:32.85667,(Ectocentrites:9.433334,(Adnethiceras",
 ":8.166656, Galaticeras:14.766663)clade_87:8.166672,((Protetragonites:56.933334,Lytoceras:5",
 "0.833336)clade_89:50.833344, Pleuroacanthites:4.666672)clade_88:4.666656)Pleuroacanthitida",
 "e:4.666667,Pterolytoceras:65.100006) Psiloceratida:18.222214)clade_26:18.222229,((Juraphyl",
 "lites:6,Nevadaphyllites:6,Togaticeras:6, Tragophylloceras:12.600006)Juraphyllitidae:6,Hypo",
 "rbulites:107.300003,(Adabofoloceras:25.400009, Hypophylloceras:121.100006,Ptychophyllocera",
 "s:56.600006,Salfeldiella:56.600006,Holcophylloceras:61.150009, Phylloceras:121.100006,Leio",
 "phylloceras:46.800003)Phylloceratidae:15)Phylloceratida:45.444443)clade_25:18.222214) clad",
 "e_22:5.066681,(Paranannites:11.566666,(Proarcestes:8.383331,Ptychites:8.383331)clade_94:8.",
 "383331) clade_93:11.566681)clade_21:5.06665)clade_15:7.100006,(Deweveria:33.300003,Juvenit",
 "es:33.300003,(Cibolites:11.5, Kingoceras:22.5,Meitianoceras:24.199997,Paraceltites:4)Parac",
 "eltitidae:4,Preflorianites:33.300003, Xenodiscus:33.300003)Xenodiscoidea:2)clade_14:2,Cart",
 "eria:37.300003,Courtilloticeras:37.300003, Eschericeratites:37.300003,Tapponnierites:37.30",
 "0003)Ceratitida:101.025024,(((Daraelites:76.399994, Epicanites:23.299988,Praedaraelites:15",
 ")Daraelitidae:28.300018,(Becanites:19.900024,Dombarocanites:47.100006, Eocanites:19.900024",
 ",Merocanites:22.400024,Prolecanites:4.5)Prolecanitidae:4.5)Prolecanitina:1,((Neopronorites",
 ":7, Sakmarites:14)Pronoritidae:17.5,(Artinskia:4.5,Bamyaniceras:34.5,Medlicottia:40.5,Prop",
 "inacoceras:31.5,Synartinskia:20, Uddenites:4.5)Medlicottiidae:4.5)Medlicottiina:66.700012)",
 "Prolecanitida:14.825012)clade_3:14.824982, (((Raymondiceras:6,(Dimeroceras:5,Paratornocera",
 "s:5)Dimeroceratidae:5)Dimerocerataceae:10,((Acrocanites:7, Jdaidites:7)Acrocanitidae:16.40",
 "0024,Kazakhstania:25.900024,Praeglyphiloceras:8,(Imitoceras:10.900024,Prionoceras:4, Triim",
 "itoceras:19.400024)Prionoceratidae:4,(Maeneceras:1,Sporadoceras:4)Sporadoceratidae:4)Prion",
 "ocerataceae:12, (Pseudoclymenia:5,(Discoclymenia:4.5,Posttornoceras:4.5)Posttornoceratidae",
 ":4.5)Tornocerataceae:11)Tornoceratina:10, (Popanoceras:117.533356,((Epitornoceras:28,Falci",
 "tornoceras:28,Lobotornoceras:6.300018,Protornoceras:5, Tornoceras:18.100006)Tornoceratidae",
 ":0.666656,(Cheiloceras:13,Torleyoceras:13)Cheiloceratidae:15.666656, Polonoceras:28.666656",
 ")Cheilocerataceae:0.666687,((((Kargalites:30.344452,(Adrianites:22.5,Nevadoceras:11, Veruz",
 "hites:11)Adrianitidae:19.344452)clade_122:19.344452,Pintoceras:25.78891)clade_121:25.78887",
 "9, ((Waagenoceras:53.14447,((Metalegoceras:9,Pericycloceras:12)Metalegoceratidae:9.5,Uralo",
 "ceras:14) Neoicoceratoidea:25.64447)clade_125:25.64444,((Branneroceras:3,Diaboloceras:10.6",
 "49994,Paralegoceras:63.600006, Schistoceras:38.100006)Schistoceratidae:3,(Wellerites:10.64",
 "9994,Winslowoceras:3)Welleritidae:3) Schistocerataceae:17.188904)clade_124:17.188873)clade",
 "_120:17.188904,(Antegoniatites:9,Habadraites:9, Primogoniatites:9,Progoniatites:9)Goniatit",
 "idae:17.866699)clade_119:17.866669,(Dzhaprakoceras:23,(Follotites:18.5, Muensteroceras:10,",
 "Xinjiangites:10)Muensteroceratidae:2,(Ammonellipsites:12.5,Helicocyclus:10,Nodopericyclus:",
 "10, Ouaoufilalites:10,Pericyclus:10)Pericyclidae:10.5,(Eurites:10.25,Mouydiria:10.25,Rotop",
 "ericyclus:10.25) Rotopericlydae:10.25,(Jerania:6,Kusinia:6,Temertassetia:6)Temertassetiida",
 "e:14.5)Pericyclaceae:24.233368, Stacheoceras:136.033356)Goniatitina:0.666667)Goniatitida:9",
 ".649994)clade_2:9.649994,(Gyroceratites:14.799988, ((Teicherticeras:8.93335,((((Probelocer",
 "as:36,(Timanites:12.600006,(Darkaoceras:2.5,Keuppites:2.5)Taouzitidae:2.5, (Gogoceras:10.1",
 "00006,Pseudoprobeloceras:2.5)Ponticeratidae:2.5,(Beloceras:9,Mesobeloceras:9) Beloceratida",
 "e:3.600006,(Archoceras:23.399994,Manticoceras:8,Mixomanticoceras:8,Sphaeromanticoceras:8) ",
 "Gephuroceratidae:4.600006)Gephurocerataceae:8)Gephuroceratatina:1.033325,Agoniatites:14.03",
 "3325) clade_144:1.033325,Celaeceras:6.866669)clade_143:1.033325,((Werneroceras:0.399994,(S",
 "obolewia:0.200012, (((Cyrtoclymenia:2.5,Clymenia:2.5)Clymeniina:2.5,Protoxyclymenia:5,Plat",
 "yclymenia:5)Clymeniida:21.066681, (Lunupharciceras:1.533325,Pharciceras:9.133331,Stenophar",
 "ciceras:1.533325,Synpharciceras:1.533325) Pharciceratatina:1.533356)clade_154:1.533325)cla",
 "de_153:0.199982)clade_152:0.200002,Anarcestes:5) Anarcestina:11.099976)clade_142:1.033356)",
 "clade_141:1.033325,Anetoceras:9.966675)clade_140:1.03333) Agoniatitida:7.100006)clade_1;")

ammoniteTreeRaia <- read.tree(text = ammoniteTreeRaia)

# what about the root age?
# Raia et al. are unclear
 # however... ahandful of taxa are known to last occur at the end-Cretaceous mass ext
 # Phylloceras
#
# Latest occurring tips are:
ammoniteTreeRaia$tip.label[
 which(node.depth.edgelength(ammoniteTreeRaia) == max(node.depth.edgelength(ammoniteTreeRaia)))]
#
# so we can treat distance of Phylloceras from root + end Cretaceous (66.043 Ma) as $root.time
(ammoniteTreeRaia$root.time <- 66.043+
 node.depth.edgelength(ammoniteTreeRaia)[which(ammoniteTreeRaia$tip.label == "Phylloceras")])

# now let's plot it
plot(ladderize(ammoniteTreeRaia));axisPhylo()


## Not run: 

# and let's load trait data from Raia et al. Appendix B:
 # FD = fractal dimension of first suture (suture complexity)
 # Log D = log of the mean shell diameter per genus (body size)
 # log dur = log of the stratigraphic duration in million years.
ammoniteTraitsRaia <- read.table("ammoniteTraitsRaia.txt",row.names = 1,header = TRUE)

sutureComplexity <- ammoniteTraitsRaia$FD
shellSize <- ammoniteTraitsRaia$Log_D
names(shellSize) <- names(sutureComplexity) <- rownames(ammoniteTraitsRaia)

plotTraitgram(tree = multi2di(ammoniteTreeRaia), trait = sutureComplexity,
  conf.int = FALSE, main = "Ammonite Suture Complexity")

plotTraitgram(tree = multi2di(ammoniteTreeRaia), trait = shellSize,
  conf.int = FALSE, main = "Ammonite Shell Diameter")


## End(Not run)

########################################
# ceratopsian species

ceratopsianTreeRaia <- paste0("((((((((((((Centrosaurus_apertus:5.1,Styracosaurus_alberte",
 "nsis:5.9):1,(((Pachyrhinosaurus_perotorum:10.5,Pachyrhinosaurus_lakustai:7):0.5,Achelousau",
 "rus_horneri:6.3):0.5,Einiosaurus_procurvicornis:6.5):1):0.5, Avaceratops_lammersi:5.5):0.5",
 ",Diabloceratops_eatoni:3):1.1,((Chasmosaurus_russelli:1.4,Chasmosaurus_belli:1.6):2.5, (Mo",
 "joceratops_perifania:3.7,(Agujaceratops_mariscalensis:1.9,((Pentaceratops_sternbergii:3.5,",
 " Utahceratops_gettyi:1):1.5,((Vagaceratops_irvinensis:1.3,Kosmoceratops_richardsoni:1):0.4",
 ",(Anchiceratops_ornatus:3.9, (Arrhinoceratops_brachyops:3.9,(Torosaurus_latus:3,(Tricerato",
 "ps_horridus:2, Triceratops_prorsus:2):1):6):0.5):1.7):1):0.5):0.5):0.5):3.8):12.9,(Bagacer",
 "atops_rozhdestvenskyi:17, (Protoceratops_hellenikorhinus:9.5,Protoceratops_andrewsi:9.5):1",
 "2):4.5):6,(Prenoceratops_pieganensis:21, Leptoceratops_gracilis:31.6):4.5):7.5,Archaeocera",
 "tops_oshimai:6):5,Auroraceratops_rugosus:15):21, Liaoceratops_yanzigouensis:6):4,(Hongshan",
 "osaurus_houi:9,(Psittacosaurus_mongoliensis:33.5, (Psittacosaurus_meileyingensis:20,(Psitt",
 "acosaurus_major:7.5,(Psittacosaurus_gobiensis:21,(Psittacosaurus_sinensis:24, Psittacosaur",
 "us_neimongoliensis:18):1):1.5):0.5):0.5):0.5):1):23,Yinlong_downsi:6):3;")

ceratopsianTreeRaia <- read.tree(text = ceratopsianTreeRaia)

# Raia et al. placed origin of ceratopsians at ~163 Ma, base of Oxfordian
ceratopsianTreeRaia$root.time <- 163

plot(ceratopsianTreeRaia);axisPhylo()

###############################################
# cervid species

cervidTreeRaia <- paste0("((((Lagomeryx_parvulus:9.925998,Lagomeryx_pumilio:10.775998):3.",
 "25,(Procervulus_flerovi:11.425998,Procervulus_dichotomus:7.025998,Procervulus_praelucidus:",
 "5.675998):3.25,(Stephanocemas_aralensis:6.925998, Stephanocemas_thomsoni:11.175998):2):2,(",
 "((Euprox_furcatus:14.440997,Euprox_minimus:12.590997, Euprox_dicranoceros:14.190997):2.185",
 "001,Heteroprox_larteti:12.175998):1.5,Muntiacus_muntjak:25.531498):1.5):1.5, (((((Alces_la",
 "tifrons:7.151589758,Alces_alces:7.245998):2.29,Cervalces_scotti:9.525768):6.64, Rangifer_t",
 "arandus:16.175998):4.35,(Procapreolus_loczyi:17.840998,Capreolus_capreolus:17.905998):2.62",
 "5):5.25, (((Cervavitus_novorossiae:9.109332,Cervavitus_variabilis:9.379332):7.149999, Plio",
 "cervus_pentelici:13.069331):2.966667,(((((Dama_clactoniana:5.133775345,Dama_dama:5.199332)",
 ":2.903333, (Pseudodama_farnetensis:5.860846548,Pseudodama_lyra:4.242887928, Pseudodama_nes",
 "tii:5.762011259):2.083333):4.166667,(Eucladoceros_ctenoides:6.892665, Eucladoceros_dicrani",
 "os:7.692563015):4.166667):2.083333,((Cervus_elaphus:5.734332,Cervus_nippon:5.744332, Rusa_",
 "timorensis:5.740332,Rusa_unicolor:5.744332,Cervus_duvaucelii:5.671332):3.4, Croizetoceros_",
 "ramosus:7.834332):5.208333):2.083333,((Praemegaceros_verticornis:9.610727017, (Megaceroide",
 "s_obscurus:6.084504245,Megaceroides_solilhacus:6.725161676):2.883334):2.883333, (Megalocer",
	"os_savini:7.349060017,Megaloceros_giganteus:7.430999):5.145):3.849999):6.6):2.75):2.75);")

cervidTreeRaia <- read.tree(text = cervidTreeRaia)

# Many of the latest-occurring tips are still extant, like Rusa unicolor and Dama dama:
cervidTreeRaia$tip.label[
	which(node.depth.edgelength(cervidTreeRaia) == max(node.depth.edgelength(cervidTreeRaia)))]

# note!
# if you plot the tree there seem to be a lot more taxa that are *almost* as late-occurring
	# unclear if this is recently extinct taxa, computational rounding error, or what

# so we can treat distance of Dama dama to root as $root.time
(cervidTreeRaia$root.time <- 
	node.depth.edgelength(cervidTreeRaia)[which(cervidTreeRaia$tip.label == "Dama_dama")])

plot(cervidTreeRaia);axisPhylo()


## Not run: 

save.image("RaiaCopesRule.rdata")


## End(Not run)

dwbapst/paleotree documentation built on Aug. 30, 2022, 6:44 a.m.