From Clone to Bone: the Synergy of Morphological and Molecular Tools in Palaeobiology Edited by Robert J

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Cambridge University Press 978-1-107-00326-2 - From Clone to Bone: The Synergy of Morphological and Molecular Tools in Palaeobiology Edited by Robert J. Asher and Johannes Müller Index More information

Index

aardvark, 39 afrotherian. See Afrotheria acanthodian, 182 and affinities of Afrodon, 51 scales, 153 Afrotherian Acanthoracida, 193 thoracolumbar count, 241 Acanthostega, 314 agnathan, 11, 169, 183 polydactyly, 305, 317 derivation of jaws, 183 Acanthothoraci, 194 pharyngeal denticles, 183 Achoania, 195 pharyngeal teeth, 139 acipenserid. See Acipenseridae Akmonistion, 180, 182 polyploidy, 157 Alcinonyx, 241 scales, 153 algae, 125 Acipenseridae, 154 alligator. See Alligator mississippiensis actinopterygian, 4, 9, 135, 154. Alligator mississippiensis, 343 See Actinopterygii allometry, 106 basal forms, 142 in mammal dentary, 211 dentition, 185, 190, 199 allotherian replacement, 195 relationships of, 50 dermal denticles, 198 Ambondro mahabo, 49, 58 ectodysplasin signalling in, 138 Amia, 195 fins, 149 amniote, 26, 27, 28 pectoral, 137 atlas/axis complex, 245 relationships with other vertebrates, 38 caudal vertebrae, 243, 247 scale development, 153 conserved body plan, 280, 292 Actinopterygii, 2, 185 digit reduction, 343 actualism, 9, 136 embryonic pharyngeal pouches, 292 adapisoriculid, 51 limb development, 261, 262 and affinities of Afrodon, 51 polydactyly, 305 Adapisoriculus, 51 prepollex/prehallux, 307 adaptation relationships of, 279 rate of, 83 relationships with other vertebrates, 2–4, 38 adaptive landscape, 84 ribs, 279, 282, 283 adaptive radiation, 60, 62 scapula, 286 Afrodon, 51 vertebral number, 147 Afrosoricida, 55, 57 Wolffian ridge, 289 afrosoricidan. See Afrosoricida amphibian, 2, 4, 25 Afrotheria, 39, 48 body elongation, 144 apomorphies of, 51 dentition, 177 relationships of, 39 prepollex/prehallux, 307

© in this web service Cambridge University Press www.cambridge.org Cambridge University Press 978-1-107-00326-2 - From Clone to Bone: The Synergy of Morphological and Molecular Tools in Palaeobiology Edited by Robert J. Asher and Johannes Müller Index More information

364 Index

Anas species selection in, 127 domestica, 353 artiodactyl, 39 platyrhynchos, 343, 353 thoracolumbar count, 241 Anaspida, 169 Australidelphia, 50 Andreolepis, 192 australidelphian. See Australidelphia Andreyevichthys, 196 dispersal into Australia, 53 angiosperm, 25 Australosomus, 154 Anguilliformes, 152 australosphenidan, 44 anlagen, 302, 305 Aves, 9, 26, 27 of avian digits, 304 cell-labelling studies, 285 of dentary, 213 dermal skeletal elements, 285 of turtle carapace, 281, 289, 293 digit identity, 311 of turtle scapula, 287 wing development. See avian wing anteater. See Tamandua tetradactyla avian hindlimb Antiarchi, 193, 194 metatarsals II-IV, 340 anuran, 306 tarsometatarsus, 340 limb development, 270 avian wing, 138, 328–55 ape, 5 anterior necrotic zone, 347 Aphanius anatoliae, 152 apical ridge. See Apical Ectodermal Ridge Apical Ectodermal Ridge (AER), 349 (AER) in the marsupial forelimb, 261, 262–4 carpometacarpus, 338, 340 in the marsupial hindlimb, 264 carpus, 328, 329–34 polydactyly, 310, 313 distal carpus, 334–8 resemblance to carapacial ridge, 289 metacarpals, 334–8 apoptosis, 315 proximal carpus, 335 in chickens, 146 cell death, 347–8 in limb patterning, 310, 311 chondrogenic foci, 355 in marsupial limbs, 264 claws, 340, 348, 351 Apteryx, 354 comparison with hindlimb, 340 australis, 354 digit, 314, 328 owenii, 354 digitus alulae manus, 329, 346 archaeocete, 243 digitus majoris manus, 329 Archaeopteryx lithographica, 338, 352 digitus minoris manus, 329, 343 digit reduction, 340 ectopic digit, 344 phalangeal formula, 352 digit homology, 304–5, 339–54 archosaur, 2, 340, 347. See Archosauria digit phenotype, 340, 348–54 digit reduction, 340 digit position, 339 digits, 353 digit reduction, 340 relationship to turtles, 279 by claw loss, 352 Archosauria, 340 by phalangeal loss, 352 Arthrodira, 193, 194 by size reduction, 352 arthrodiran. See Arthrodira comparison with non-avians, 346 dentition, 193 element X, 339 dentition development, 195 embryonic hexadactyly, 345 arthropod, 247 embryonic pentadactyly, 345 molecular clock, 55 frame shift, 305, 343, 355

Index 365

handplate, 348 genome intercalary element, 348 chromosome type, 27 mesopodium, 329 repetitive elements in, 26 metacarpals, 338, 346 size of, 25–6 nomenclature, 330–5 molecular clock, 55 os carpi radiale, 335 relationship to theropod dinosaurs, 9 os carpi ulnare, 335 relationship to turtles, 279 phalangeal formula, 352–4 relationships with other vertebrates, phalanx-forming region, 355 2–4 pisiform, 335 sacrum, 245 postminimus, 346 secondary cartilages, 212 pre-axial polydactyly, 344 wing development, 9. See avian wing prepollex, 346 Birgeria primary axis, 343–4 stensioï, 144, 147 processus extensorius, 346 bivalve, 91 processus pisiformis, 339 bony fish, 2, 4 radiale, 335 boreosphenidan, 44 radius, 328 Bothriolepis, 193 rescue of digit I, 344 Bradypus, 237 ulna, 328, 335 Branchiostoma, 2 ulnare, 335 Bustylus, 51 ungual, 349 butterfly fish, freshwater. See Pantodon wrist, 328. See mesopodium buchholzi Zone of Polarizing Activity, 348 axial skeleton, 95 caecilian, 2 of mammals, 8, 230–48 body elongation, 144 of Saurichthys, 10, 159 Cairina moschata, 353 axolotl, 177 Calchides, 347 Callichthyidae, 154 basilosaurid, 243 Callorhinchus. See chimaera bat, 68, 230, 257 Caperea, 237 limbs, 301 marginata, 239 forelimb development, 268 Capromys pilorides, 57 wing, 138 capybara. See Hydrochoerus bear, 122 Carcharinidae, 180 Belonidae, 150 Carnivora, 38, 152 bichir, 144. See polypterid face length, 151, 159 bird, 100, 311, 329, 352. See Aves thoracolumbar count, 241 beaks, 151 carnivoran. See Carnivora conservation of odontogenic signalling carnivore pathways, 167 prehallux, 306 digit reduction, 351 prepollex, 306 evolutionary rate, 97 thoracolumbar count, 241 feather development, 178 carp feather patterning, 179 scales, 152, 157, 159 flight, 97 carpalia, 331

366 Index

carpus necrotic zones of limb, 347, 348 of birds, 329–34 pisiform, 347 of urodeles, 330 primary axis, 343 3 3 cartilaginous fish, 2, 4 talpid (ta ) mutant, 310 Cassuarius cassuarius, 354 wing development, 305, 328, 355 catfish, 152 chimaera, 138 catfish, armoured, 154 Chinese soft-shelled turtle. See Pelodiscus catshark, 150 sinensis cave bear. See Ursus spelaeus chiropteran Caviidae, 347 os falciforme, 309 centrale, 331 prepollex, 306 Cercopithecus, 243 Chlamydoselache, 182 Cetacea Chlorurus, 124 absence of pelves, 233 Choloepus, 237 origin of, 64 didactylus, 347 cetacean. See Cetacea hoffmanni, 237, 347 body size, 62 chondrichthyan caudal vertebrae, 243 dental lamina, 182, 189 fluke, 243 dentition, 179, 193 increased lumbar count, 242 dermal denticles, 177, 179, 198 polydactyly, 305 ectodysplasin signalling in, 138 rate of molecular evolution, 55 heterodont dentition, 169 Cetartiodactyla, 39, 48 pharyngeal denticles, 183 apomorphies of, 50 placoid denticles, 173 Chalcides chalcides, 343, 352 scale patterning, 198 chicken, 10, 27, 328, 344, 353. See Gallus scale replacement, 179 apoptosis, 146 tooth development, 167 BAMBI expression, 352 Chondrichthyes, 2, 193 chick chondrification Apical Ectodermal Ridge, 262 in limb development, 304, 310 axial skeleton, 148 chordate, 2, 8 dentition, 171, 197 species selection in, 127 jaw articulation, 207 chrysochlorid, 47 limb development, 270 cichlid, 10, 169, 171 limb position, 149 dentition, 192, 197 phalangeal formula, 354 development, 184, 186 tooth restoration in, 167 diversity of, 171 dentary, 224 pharyngeal, 176, 183 distal carpus, 338 jaws, 151 ectopic digit, 344 tooth shape diversity, 185 element X, 339 cingulate, 47 foot, 349 clam, 92 frame shift, 343 claws genetic mechanisms, 136 in birds, 340, 352 induction of phalanges, 351 in crocodilians, 352 limb position, 149 in fossil birds, 352

Index 367

in hoatzin, 353 in vertebrates, 283 in Neornithines, 352 desman, 307 in talpid moles, 311 swimming, 307 coelacanth, 2 tibial sesamoid, 313 Coelodonta antiquitatis, 20 deuterostome, 4, 67 condylarth, 46, 47 developmental bias conodont, 169. See Conodonta in mammal axial skeleton, 231 dentition, 193, 194 developmental constraints, 305, 346 pharyngeal denticle co-option, 198 and pleiotropy, 106 odontodes, 169 in birds, 97 Conodonta, 169, 183, 193 in mammal axial skeleton, 231, 232 coral, 121, 125 in marsupial limbs, 260, 271, 273 Craniata, 311 in the notochord, 106 craniate. See Craniata in turtle shell evolution, 280 crinoid, 119 developmental genetics, 8, 9, 304 crocodile. See crocodilian Diabolepis, 196 dermal ossiﬁcation of the trunk, 283 Diacodexis, 50 relationship to turtles, 279 diapsid, 2, 26 crocodilian, 27 dentary, 224 digit reduction, 352 relationships with other vertebrates, 38 manus, 340 Didelphis, 92 primary axis, 343 digits, 9 crocodylomorph, 100, 101 development, 310 Cryptotis parva, 310, 316, 317 in marsupials, 264 Cuvier, Georges, 234 homology in birds, 339–54 cyclostome, 4 mouse, 343 cynodont of horses, 338 coronoid bone, 222 prepollux/prehallux, 306 double jaw joint, 208 reduction in ungulates, 345 cypriniform, 190 Dilambdogale gheerbranti, 47 Cyprinus carpio, 157 dinosaur, 26, 136 extinction, 61 Dactylopsila trivirgata, 215 generation time, 94 darwin (unit), 93, 94 genome size, 25 Darwin, Charles, 4, 90, 91, 98, 135, 151, 159 interrelationships with birds and Dasypus, 243 theropods, 9 Date-A-Clade, 18 dipnoan, 25 Deccanolestes, 46, 51, 54 divergence times, 104, 108 delphinoid, 244 estimation of, 18, 85–9 dermal armour, 280 in mammals, 38–70 dermal skeletal elements, 10 limitations of molecular data, 104 denticles, 199 multiple calibration points, 88, 89 in birds, 285 rate heterogeneity, 85, 86, 88 in dentition, 167 using morphological data, 104–6 in Saurichthys, 142 fossil calibration, 40, 85, 87, 88, 105 in the turtle shell, 281 fossil data

368 Index

divergence times (cont.) Doliodus, 182 assumptions of, 40–54 dolphin in crown-placental mammals, 6 hyperphalangy, 302, 349 molecular clock, 54–8 Dromaius novae-hollandae, 354 local clock, 57, 67 Drosophila, 140, 146 rate constancy, 87 dryolestoid, 47 relaxed clock, 57, 67 duck, 328. See Anas molecular data wing, 353 assumptions of, 54–70 Dugong, 242 of hominines, 5 of Laurasiatheria-Euarchontoglires, 5 Echimydae, 57 diversification rate, 7, 117 ectopic gene regulation and morphological disparity, 92 in turtles, 280, 283 Djarthia murgonensis, 50 edentate DNA, 6 prehallux, 306 ancient DNA, 6, 18, 20–1 prepollex, 306 limitations of, 22 elephant, 22, 309 cDNA, 171 elephant shrews. See Macroscelididae chromosome, 26, 27, 28 endochondral skeletal elements 22qii deletion, 219 in the turtle shell, 281 7q36, 309 Eohippus, 91 autosome, 27 Eomaia, 49 macrochromosome, 27 scansoria, 59 microchromosome, 27 epigenetic effects, 84 sex chromosome, 7 and phenotypic plasticity, 83 sex chromosomes, 27 in fish scale development, 154 copy error, 83 on morphology of the dentary, 213 epigenetic gene regulation, 21 Equus quagga exons, 21 relationships of, 19 introns, 21, 25 Eremitalpa granti, 347 linkage disequilibrium, 16 Eritherium azzouzorum, 48 long interspersed nuclear element, 26 Erpetoichthys calabaricus, 145 mitochondrial, 19–20, 55, 66 Erythrozootes, 47 point mutation, 83 Euarchonta, 51 polymorphism, 16 euarchontan. See Euarchonta recombination, 16, 83 and affinities of Afrodon, 51 repetitive elements, 25, 26 and affinities of Purgatorius, 52 reverse transcriptase, 25, 26 Euarchontoglires, 5, 39, 65 sequencing, 6 Eulipotyphla, 307 direct multiplex sequencing, 21 Eutheria, 46 single molecule sequencing, 21 earliest members, 49 short interspersed nuclear element, 26 eutherian, 39, 237. See Eutheria single nucleotide polymorphisms, 21 and affinities of Ambondro, 49 substitution rate, 86 and affinities of Deccanolestes, 51 dog, 306 Cretaceous forms, 45 polydactyly, 313 early memmbers, 50

Index 369

Gondwanan forms, 46 stabilizing selection, 98, 99, 107 origin of, 59 stochasticity in, 83, 84, 85, 86, 104, 108 South American forms, 47 extant phylogenetic bracket, 23, 137 tribospheny, 44 in Saurichthys reconstruction, 157, 158 evo-devo, 158, 225, 328, 330. See evolutionary extinction, 16, 116, 161 development in species selection, 117 evolution K/T event, 40 predictability of, 139–41 rate of, 7, 83 evolutionary canalization in sesamoid development, 309 fascia palmaris, 306 evolutionary development, 7 Fayum fauna, 47 evolutionary rate, 83–108 Felidae, 38 directional selection, 98, 99, 100 felsen (unit), 94 evolutionary constraint, 99 ferret, 171 extinction, 87 fibulare, 340 extinction rate, 89 fin to limb transition, 9, 301 in mammals, 92 Fisher, R. A., 98 genotype-phenotype correlation, 97 fissiped in bivalves, 91 os falciforme, 309 in horses, 92 frog, 2 in mammals, 91 autopodium, 313 molecular clock, 85, 100, 105 prepollex, 307 local clock, 89 rate heterogeneity, 88 Galloanserae, 329 relaxed clock, 89 Gallus, 27 molecular data, 98 gallus, 328 molecular evolution, 84, 85 Ganungulatum xincunliense, 48, 50 measuring rate of, 85–9, 90 gars. See Lepisosteidae morphological clock, 108 Gasterosteidae, 154 morphological data, 98 Gegenbaur morphological evolution, 84, 85, 100, 108 Carl, 330 darwin (unit), 93, 94 genetic drift, 83 disparity analysis, 96 genetic mechanisms, 9, 136, 139, 140 divergence time estimation, 104–6 in Drosophila felsen (unit), 94 shaven baby/ovo, 140 haldane (unit), 93 in mammal axial skeleton measuring rate of, 89–97 Hox, 8 patristic dissimilarity, 94 in pectoral fin development patristic distance analysis, 94 Hox, 137 patristic methodology, 95, 96, 105 in Saurichthys, 10, 158 stochasticity in, 98–104, 105, 107 calmodulin, 159 nearly neutral model, 99, 101 caudal, 146 neutral model, 98, 100, 104 cdx, 145 phenotypic change, 84 ectodysplasin, 157, 159 rate heterogeneity, 107 ectodysplasin signalling, 154, 157 speciation rate, 87, 89, 93 Eda, 10

370 Index

genetic mechanisms (cont.) Runx2, 152 FGF, 10 of limb development Fgf signalling, 146, 154, 157, 159 BAMBI, 351 Hox, 10, 159 BMP, 310 pleiotropy, 157 BMP signalling, 352 retinoic acid, 10, 145, 159 Fgf4, 262 runt, 159 Fgf8, 262, 270 Tbx, 10 Gli3, 348 Wnt signalling, 146 Hox, 352 in Saurichthys body elongation, 148 Hoxa13, 315 in Saurichthys ﬁn position, 148–50 hoxd, 352 in Saurichthys jaw elongation, 150–2 HoxD, 314 in Saurichthys scales, 152–8 Hoxd10, 315 of (marsupial) limb development hoxd11, 344 Fgf8, 263 Hoxd12, 305, 315 of avian wing development Hoxd13, 305, 315 BAMBI, 352 Msx, 310 fgf8, 349 in AER formation, 310 Hox, 348 in bone development, 310 hoxa13, 329 Msx1, 310 hoxd13, 329 Msx2, 310 pitx1, 344 in digit separation, 311 Sox9, 345 retinoic acid, 313 wnt14, 349 Shh, 310, 313, 315 of feather development sonic hedgehog signalling, 348 BMPs, 178 of mammal axial skeleton Fgf-4, 178 Hox, 231 follastatin, 178 homeotic variation in, 235 Ptc, 178 Hox10, 246 Shh, 178 Hox11, 246 of ﬁsh scale development of mammal axial skeleton Hox, 232 bmp2b, 179 and cervical ribs, 237 Eda, 179 regionalization of the vertebral column, Edar, 179 246 ephA4, 179 of mammal dentary, 216–20 Runx, 179 Alk2, 218 shh, 179 cre-recombinase system, 218 of hair development Dlx5, 218, 219, 222 BMP, 178 EDA, 220 ectodyplasin, 178 Gsc, 220 Edar, 178 MyoD, 219 of jaw development Pax9, 216, 218, 219, 221, 222, 223, 224 Hox, 183 Prx1, 219 of jaw elongation PTHrP, 221, 224 Bmp4, 151 Runx2, 213, 216, 220 calmodulin, 151 Sox9, 218

Index 371

Tbx1, 219, 222, 223 Fgf8, 311, 317 TCOF1, 220 Hox, 315 Tgf b 2, 216, 217 Msx, 311 Tgfb signalling, 218, 221 Msx2, 311, 317 Tgfb2, 218, 221, 224 Shh, 311 Tgfbr2, 217, 218, 220 Sox9, 310, 314, 316, 317 Tgf-b signaling, 222 of turtle shell development Tgf-b2 signalling, 223 APCDD1, 289 type II collagen, 216 BMP signalling, 283 Wnt1, 219 Hox, 281 of marsupial limb development Lbx-1, 287 Fgf8, 268 Lef-1, 289 Gli3, 268 Pax3, 287 Hand2, 268 Sp5, 289 Hoxd9, 268 Wnt, 289 Pitx1, 267 Wnt signalling, 289 Tbx4, 267 of vertebrate axial skeleton Tbx5, 267 Hox, 147 of median ﬁn position Hox12a, 148 Hoxd10, 150 Hoxc10a, 148 Hoxd12, 150 of vertebrate dentition Hoxd9, 150 Barx1, 167 Tbx18, 150 BMP signalling, 185, 187, of mouse limb development 191 HoxC10, 267 bmp2, 180, 186, 189 Tbx4, 267 bmp4, 180, 181, 186, 189, 190 Tbx5, 267 Bmp4, 185, 187 of paired appendage position BMP4, 167, 187 Gdf11, 149 dlx, 190 Hox, 149 dlx1a, 190 hoxc10a, 149 dlx2, 180, 186, 190 retinoic acid, 149 dlx6b, 190 Wnt signalling, 149 ectodin, 191 of pelvic ﬁns ectodysplasin, 186, 191 pitx1, 149 eda, 178, 180, 186, 189 Tbx4, 149 Eda, 187, 191 of somite development Eda signalling, 185 cdx, 148 edar, 180, 186, 189 Fgf, 148 ephA4, 176 Fgf signalling, 148 FGF signalling, 185, 187, 190 nodal, 148 Fgf-10, 181 retinoic acid, 148 Fgf-3, 181 t-box, 148 fgf8, 189 Wnt, 148 FGF8, 167 Wnt signalling, 148 Fgfr1b, 181 of talpid mole limb development Fgfr2b, 181

372 Index

genetic mechanisms (cont.) Glyptodon, 283 Hedgehog signalling, 185, 190 gnathostome, 2, 4, 183, 185 Hh signalling, 187 appendage patterning, 311 Hox, 183, 184 dentition, 166, 181, 195, 199 Lunatic fringe, 181 ectodysplasin, 138 Msx, 187 genetic mechanisms, 137 Msx1, 167, 187 mandible, 207 Msx2, 167 oral teeth, 139 Notch, 181 pharyngeal denticles, 183 odontode gene regulatory network, 178 relationships with other vertebrates, 38 Osr2, 187, 191 golden mole, 47 Otlx2, 167 golden mole, Grant’s, 347 pax9, 180, 186, 189, 192 gonadal steroids, 315 Pax9, 167, 187 gondwanatherian, 47 pitx2, 180, 181, 185, 186, 189 relationships of, 50 Pitx2, 167 goose, 329 Runt, 176 gorilla, 5 Runx, 176 Gorilla, 309 Runx2, 176, 180, 186, 189 Granada, Spain, 316 shh, 178, 180, 181, 185, 186, 189, 196 great ape, 5 Shh, 187, 189, 191 rate of molecular evolution, 55 TGFß signalling, 185, 190 guinea pig, 211 Wnt signalling, 181, 185, 187, 190, 191 dentary, 214, 223, 224 wnt7b, 178, 180, 186, 189 Guiya, 195 Rag-1, 4 SPAG17, 22 Haeckel, Ernst, 2, 4, 279, 304 genome hagﬁsh, 2 duplication, 139 haldane (unit), 93 mitochondrial, 54 hallux, 306 nuclear, 54 haramiyidan of elephant shark, 137 relationships of, 50 sequencing hedgehog, 307 in marsupials, 224 Helarctos, 241 genomics, 6, 11, 16, 18, 29, 30 Hemiergis, 347, 348, 349, 352 genome size, 7 hemoglobin, 5 directional evolutionary change, 25 molecular clock, 54 inference of, 25–6 Herpetotheriidae, 92 paleogenomics, 7, 16–31 heterochrony, 282 genotype-phenotype map, 84, 85, 108 in dolphin hyperphalangy, 349 genotypic sex determination in mammal dentary, 211 evolution of, 27 in marsupial syndactyly, 302 giant panda, 309, 317 in whale hyperphalangy, 302 ‘thumb’, 317 sequence heterochrony, 261 Gill, Theodore Nicholas, 2, 4 heterotachy, 22, 55, 64, 66, 69, 89 giraffe, 230 heterotopy Glires, 39 in the turtle shell, 282

Index 373

in turtles, 280 prepollex, 306 in vertebrate dentition, 176 intermedium, 331 heterotropy, 169 invertebrate, 157 hippopotamus, 191, 213 marine, 105 hoatzin. See Opisthcomos hoatzin terrestrial, 105 Holodipterus, 197 Itaborai fauna, 47 hominid, 55 hominine, 5 Juramaia sinensis, 50, 59 Homo neanderthalensis, 22 K/T boundary, 6 sapiens, 22 K/T mass extinction, 40 horse, 5, 19, 91, 338 kangaroo, 191, 257 evolutionary rate, 92 Kharmerungulatum, 46, 54 human, 5, 8, 20, 22, 26, 257. See Homo sapiens killifish, 152 cervical ribs, 237 koala, 8. See Phascolarctos cinereus dentary, 223 divergence time, 5 labrid fish, 125, 126, 130 hand, 303 pharyngeal jaws, 124 hypodontia, 187 lacunae, 25 interbreeding with Neanderthals, 22 lagomorph, 39 interrelationships of peoples, 22 lamprey, 2, 183, 184 Inuit, 22 median fin, 150 limbs, 313 unpaired fins, 149 Native Americans, 22 lateral plate mesoderm, 248 polydactyly, 309, 314 in paired appendage development, 149 prehistoric pacific islanders, 19 Laurasiatheria, 5, 39, 48, 65 Saqqaq people, 22 lepidosaur, 92 temporo-mandibular joint, 207 Lepisosteidae, 150 Huoshanornis huji, 352 Lepisosteus, 195 Hydrochoerus hydrochaeris, 347 Lineatriton, 143 hyperphalangy, 349 Lipotyphla, 39. See Eulipotyphla in tetrapods, 302 lipotyphlan. See Eulipotyphlan in turtles, 302 Lissodelphis, 242 in whales, 302 living fossils, 92 Hyracoidea, 62 lizard dentition, 197 ichthyosaur, 27 manus, 348 hyperdactyly, 302 primary axis, 343 Ichthyostega tooth replacement, 166, 189 polydactyly, 305, 317 lobe-finned fish, 2 posterior digits, 314 Loganellia, 183 Ignacius graybullianus, 51 Lophosteus, 192 Insectivora, 39 Loricariidae, 154 insectivoran, 39 lungfish, 171, 178. See dipnoan os falciforme, 309 dentition, 10, 196–7 prehallux, 306 replacement, 195

374 Index

Macroscelidea, 39, 57 from morphological data, 38, 39 mammal, 5, 10, 25, 26, 27, 28, 41, 50. relationships with other vertebrates, See Mammalia 2–4 adaptive radiation of, 62 sacrum, 245 body size, 62 tribospheny, 44 cell proliferation, 268 mammal axial skeleton, 8, 230–48 Cretaceous forms, 62 abaxial patterning, 231, 238, 239, dentition, 42, 169 240, 248 dual molecular origin, 177 abaxial structures, 231, 233 genetic mechanisms, 186–90 analogy with arthropods, 247 heterodonty, 169, 171 associational variation, 235 reduction of, 186 in caudal vertebrae, 243 reiterative signalling cascade, 167 caudal count, 243 tooth position, 185 caudal vertebrae, 230, 233 tooth replacement, 166, 181 in cetaceans, 243 tribospheny, 49 modular change in, 243–5 dentition development, 166, 171, 184 cervical vertebrae, 230, 233 genetic mechanisms of, 185 atlas, 233 dermal armour, 283 axis, 233 dermal ossiﬁcation of the trunk, 283 constraint, 237, 248 digit reduction, 346 in humans, 237 dispersal of, 53 in manatees, 239 diversity of, 257 in pygmy right whales, 239 evolution in tree sloths, 237 effect of marsupial constraint, 259 modular change in, 237–40 evolutionary rate, 91, 92, 97 cervicothoracic boundary, 233 extinction rates, 92 column series deﬁnitions, 232–4 generation time, 94 developmental constraint, 230, 231, genome 232 chromosome type, 27 homeotic variation, 235 repetitive elements in, 26 cervical ribs, 237 size of, 25–6 thoracolumbar count, 241 hair development, 178 homologous variation heterotachy, 65 in cervical vertebrae, 247 juvenile fossil material, 50 ilium, 232, 233, 243 limb diversity, 257 intercalation, 231, 239 limb evolution, 272 lumbar vertebrae, 230, 233 limb modularity, 260 modular change in, 240–3 mandible, 8 lumbosacral boundary, 233, 243 Mesozoic mammals, 100, 101 meristic variation, 235 reduction lumbar ribs, 241 in caudal vertebrae, 243 middle ear ossicles modularity, 234–5, 248 homologues in tetrapods, 207 homologous variation, 235 polydactyly, 305, 306 pelvic girdle, 233 relationships of, 38–70 presacral count, 241 from molecular data, 39 primaxial patterning, 231

Index 375

primaxial structures, 231, 233 marsupial neonate jaw articulation, 208 primaxial-abaxial shift, 238, 239 micrognathia, 219 redivision, 231 modularity, 209–10 sacral vertebrae, 230, 233 morphological units, 210 modular change in, 243 alveolar bones, 210 sacrum, 233, 243 angular process, 210 segmentation clock, 231, 244 condylar process, 210 somite clock, 235 mandibular body, 210 somitogenesis, 235 mental/rostral process, 210 sternum, 232, 233, 241 proximal coronoid, 210 thoracic vertebrae, 230, 233 secondary cartilages, 210 modular change in, 240–3 morphological variation of, 210–13 thoracolumbar count musculature, 208 conservation of, 241 neural crest, 218, 219 thoracolumbar differentiation, 241 postdentary bones, 208, 222 transposition, 231 hearing, 208 mammal dentary, 207 homologues in tetrapods, 207 angular process, 209 rat, 221 in common shrews, 211 secondary cartilages inﬂection in marsupials, 212, 213, 215 in human, 212 lack of in humans, 212 in mice, 212 placental mammal, 213 in rats, 212 changes during development, 213–16 sesamoid bones, 212 condylar process, 209 squamosal-dentary joint, 207 coronoid process, 209 selection pressure, 208 in guinea pigs, 211 unilateral occlusion, 208 in mice, 211 Treacher Collins syndrome, 220 in rabbits, 211 tympanic ring, 213 in weasels, 211 velocardialfacial syndrome, 219 reduced integration of, 221–2 X-linked Hypohidrotic ectodermal development dysplasia, 220 in guinea pigs, 214 mammal divergence times, 38–70 in mice, 213 and paleobiogeography, 53–4 DiGeorge syndrome, 219 crown-group diversiﬁcation, 40 ectotympanic, 213 crown-group origin, 40 effect of ecology on morphology fossil data in carnivores, 223 apomorphy lag, 48, 52 in herbivores, 212 assumptions of, 40–54 in humans, 213 character funnel, 43, 44 in mice, 212 explosive model, 53, 65 in omnivores, 212 gaps, 45–8 in rats, 212 ghost lineage, 52 genetic mechanisms, 216–20 induction ratchet, 44, 45 human syndromes, 220 long-fuse model, 67 in mice, 216–20, 221 morphological clock, 52 jaw musculature, 221 phylogenetics, 48–52

376 Index

mammal divergence times (cont.) reproduction, 257 short-fuse model, 67 sexual dimorphism, 302 from morphological characters, 41–5 syndactyly, 302 molecular data tooth replacement, 51 and fossil calibration, 58–60 marsupial limbs, 10, 257–72 assumptions of, 54–70 development fossil calibration, 67, 68 anterior-posterior patterning, 268, 271 local clock, 57, 67 Apical Ectodermal Ridge, 271 molecular clock, 54–8, 68 apoptosis, 264 neutral theory, 54 cell proliferation, 264 quality of, 67–70 chondrogenic events, 260 relaxed clock, 57, 60, 67 gene expression, 265–70, 271 molecular evolution independence of fore-/hindlimb rate of, 55, 60–7 development, 260–5 Mammalia, 49, 70 prechondrogenic events, 260, 261 crown-group root, 50 proximal-distal patterning, 268 digit reduction, 346 developmental constraint, 260, 270, 271 divergence times, 40 forelimb, 258, 260–4 mammaliaform, 53, 208. See Mammaliaformes accelerated development, 261 coronoid process, 222 Apical Ectodermal Ridge, 261, 268, 271 Mammaliaformes, 43 developmental constraint, 273 mammoth. See Mammuthus molecular AER, 263 mammoth, woolly, 22. See Mammuthus physical AER, 262 primigenius hind limb, 264–5 Mammut americanum, 23 Apical Ectodermal Ridge, 262, 264 Mammuthus primigenius, 20 delayed development, 264 manatee. See Trichechus in neonates, 260 cervical vertebrae, 239 microarray assay, 265–70 maniraptoran, 96, 338 modularity, 260 Manis tetradactyla, 243 pelvis, 257 manus reduced fore-/hind limb covariation, 259, avian, 354 262, 264, 268, 270, 271 marine reptile, 27, 241 scapula, 257 marsupial, 8, 10 selection pressures on, 259 American marsupials, 261, 264 shoulder girdle, 257, 258 angular process inﬂection, 212, 213, 215 mastodon. See Mammut americanum Australian marsupials, 261, 264 maximum likelihood, 121 divergence time, 49 Meckel’s cartilage, 207 diversity of, 257 medaka, 138 epipubic bones, 43 dentition, 186 genome, 224 pattern, 179 morphological diversity, 257 tooth initiation, 190 neonate, 257, 271 scales, 154, 159 jaw articulation, 208 membranous bone, 282 os falciforme, 309 Mephitis, 241 postcanines, 49 mesenchyme condensation

Index 377

in limb development, 304 forelimb mesoderm, 8 Apical Ectodermal Ridge, 261, 262, 263, lateral plate mesoderm, 8 271 somitic mesoderm, 8 hind limb Metatheria Apical Ectodermal Ridge, 262 earliest members, 49 limb development metatherian. See Metatheria anterior-posterior patterning, 270, 271 of South American, 47 apoptosis, 264 Metazoa, 104 cell proliferation, 264 metazoan. See Metazoa fore-/hind limb covariation, 268 mice. See Mus gene expression, 265, 268 microarray, 10, 263 transcriptome, 273 mineralization Monodelphis domestica, 10, 224, 261, 271, 273 in limb development, 304 monotreme, 44, 47 minnow and afﬁnities of Ambondro, 49 scales, 152 divergence of, 50 minnow, naked, 154 limb covariation, 259 mitochondria prehallux, 306 endosymbiotic theory of, 18 relationships of, 50 genome of, 19, 20, 21 tibiale, 307 sequencing of, 19–20 Morganucodon moa, 20 double jaw joint, 208 modern synthesis, 91 MorphoBank, 42 mole, 9, 306, 307–16. See talpid mole Morse’s law, 346 shrew mole, 307 mosasaur, 27 Sox9 expression, 311 mouse, 10, 224, 311, 317 molecular clock, 5 axial skeleton, 148 early application of, 5 caudal-related genes, 146 limitations of, 6 dentary, 225 molecular mechanisms, 9, 135, 137, 159 coronoid process, 211 in denticle development, 183 development of, 213 in marsupial limb development, 271 genetic mechanisms, 216–20 in Saurichthys, 135–59 secondary cartilages, 212, 222 in vertebrate dentition, 171, 187, 197 Tgf-b2 knockout, 217 molecular reconstruction, 136–41 Tgfbr2 knockout, 218 actualism, 136 dentition, 171, 176, 177, 224 in Saurichthys, 158 replacement, 181 parsimony, 136 dentition development, 167, 169, 171, 184, uniformitarianism, 136 197 molecular systematics genetic mechanisms of, 180, 186–90, 191 and species selection, 130 digits, 343 mole’s thumb, 9, 307–16 genetic mechanisms, 136 Hox gene expression, 315 gonadal steroids, 314 mollusc limb development, 305, 352 species selection in, 127 anterior-posterior patterning, 270 Monodelphis, 10, 224, 268 Apical Ectodermal Ridge, 262, 263

378 Index

mouse (cont.) as origin of turtle costal plates, 285–6 apoptosis, 264 homology, 304 cell proliferation, 264 in dentary development, 218 fore-/hind limb covariation, 268 in jaws, 183 gene expression, 265, 267, 271 elongation of, 151 limb position, 149 in mammal dentary, 219 middle ear ossicles, 207 in tooth development, 166 polydactyly, 310 in vertebrate dentition, 177 prepollex/prehallux, 307 odontogenic capacity, 177 mouse, beach, 140 neutral theory, 54, 97, 98 mouse, pocket notochord, 145, 292 melanism, 140 developmental constraint, 106 mRNA, 146 Numenius, 353 multituberculate, 58 relationships of, 50 Odontochelys, 9, 290, 293 muraena, 152 carapacial ridge, 290 murid. See Muridae neural plates, 282 dentition, 186 scapula, 290 Muridae, 212 semitestacea, 9 Murtoilestes abramovi, 59 serratus anterior, 290 Mus. See mouse odontode Mus musculus, 213, 224, 312. See mouse homology, 178 development Oncorhynchus mykiss, 189 anterior-posterior patterning, 271 Ophidiiformes, 152 limb development Opisthcomos hoatzin, 353 apoptosis, 264 opossum, 92 cell proliferation, 264 opossum, short-tailed, 224. See Monodelphis limb transcriptome, 273 domestica Musculus abductor pollicis longus oral teeth, 199 in association with sesamoid, 309 organogenesis in primates, 309 in turtles, 280 myocytes, 20 Osborn, H. F., 91 myotome, 282, 283 osetoglossomorph, 92 osteichthyan, 192 Neanderthal, 21, 22. See Homo neanderthalensis dentition, 196 nearest neighbour hypothesis, 179 development, 167 needleﬁsh. See Belonidae heterodonty, 169 Neoaves, 329 pattern, 179 origin, 59 pharyngeal denticles, 183, 195 Neoceratodus, 178 replacement, 195 forsteri, 196 postbranchial lamina, 195 Neoceratodus forsteri. See lungﬁsh osteoarthritis, 313 neocete, 244 osteoderms Neognathae, 328 in pariesaurs, 283 Neornithe, 335, 352 in xenarthra, 47 neural crest, 310 Osteostraci, 169

Index 379

ostrich, 339, 353. See Struthio camelus Phoxinellus, 154 claws, 354 phylogenetic consensus, 4–5 digit size reduction, 351 phylogenetics pseudoulnare complex, 339 Bayesian methods, 23, 69, 86, 87, 88, 89, 101, oyster, 92 106, 107 from fossil data, 48–52 paddlefish. See polyodontid ghost lineages, 96 paenungulate, 39 maximum-likelihood, 86, 87, 106, 107 palaeanodont, 47 parsimony, 86, 95, 99, 100, 105 Palaeognathae, 329 stratigraphic debt, 96 Palaeospondylus, 136 temporal paradox, 95 Panderichthys, 314 phylogeography, 20 Pantodon buchholzi, 92 pika, 65 Parageogale, 47 pipefish, 154 Parareptilia, 279 pisiform, 339, 346, 347 pareiasaur, 280 placental mammal. See Placentalia dermal armour, 283 adaptive radiation of, 62 relationship with turtles, 283 angular process, 212 parrotfish, 124, 125 divergence time, 45, 46, 70 sexual dichromatism, 125 explosive model, 44, 48 parsimony, 9 long-fuse model, 67 Patterson, Colin, 1, 2, 4, 7, 8, 169 of crown, 6 pearlfish, 152 short-fuse model, 67 pectoral fins diversity of, 257 in sarcopterygians, 314 heterotachy, 65 Pedetes, 306 morphological diversity, 257 capensis, 306 paleogeography, 45, 46 Pelodiscus sinensis, 285, 290 postcanines, 49 penguin, 353 placental mammal limbs, 272 pentadactyl limb, 355 apoptosis, 264 pentadactyl manus, 339, 340 cell proliferation, 264 pentadactyly constraint, 313 development of Perciformes, 152 gene expression, 267 Peristediidae, 154 prechondrogenic events, 261 phalangeal formula fore-/hind limb covariation, 259, 268, 270 in Archaeopteryx lithographica, 352 forelimbs, 268 in birds, 353 gene expressoin, 271 in crocodilians, 352 hind limb, 264 in Huoshanornis huji, 352 shoulder girdle, 257 in reptiles, 353 placental mammal/marsupial split, 49 phalanx-forming region, 349 Placentalia, 40, 46, 52 pharyngeal teeth, 199 initial differentiation, 53 Phascolarctos cinereus, 215 placoderm. See Placodermi phenotypic plasticity, 83, 95 dental lamina, 182, 189 Phocoenoides, 242 dentition, 193–4, 195 phospho-histone H3, 265 replacement, 195

380 Index

placoderm. (cont.) protein preservation, 22–3 dentition development, 195 protostome, 67 genetic mechanisms, 137 Protungulatum, 48 pharyngeal denticles co-option, 198 Psammobates geometricus, 347 postbranchial lamina, 194 Psarolepis, 195 Placodermi, 10, 169, 193, 194, 195 pufferfish, 152 placoid denticles, 173 punctuated equilibrium, 118 plant Purgatorius, 52 species selection in, 127 pygmy right whale, 239. See Caperea pleiotropy, 237, 305 python, 171 constraint on development, 106 in Saurichthys, 157 quail, 224, 295 plesiadapiform. See Plesiadapiformes and affinities of adapisoriculids, 51 rabbit, 65, 92, 211, 223 Plesiadapiformes, 51 radiale, 331 Plotus, 353 ragfish, 152 polar bear, 20 Ramapithecus, 5 polydactyly, 313 raptor, 27 caused by gonadal steroids, 314 rat, 306 in dogs, 313 secondary cartilages of dentary, 212 in humans, 309 ratite, 20 polyodontid, 142 wing, 348 polypterid, 142, 144 ray-finned fish. See Actinopterygii Polypterus, 145, 198, 199 Reichert, Karl, 207 possum, 257 relationships possum, striped. See Dactylopsila trivirgata of actinopterygians, 38 possum, Western Australian honey. of Afrotheria, 39 See Tarsipes rostratus of allotherians, 50 postbranchial lamina, 198 of amniotes, 38, 279 Price’s theorem, 117, 130 of archosaurs, 279 primate, 44, 51 of birds, 9, 279 crown-group origin, 58 of crocodiles, 279 dentition development, 185 of diapsids, 38 molecular clock, 55 of Equus, 19 monophyly, 66 of gnathostomes, 38 prehallux, 306 of gondwanatherians, 50 prepollex, 306 of haramiyids, 50 sesamoid, 309 of mammals, 38–70 primitive streak, 245 of monotremes, 50 Proboscidea, 48 of multituberculates, 50 Prochrysochloris, 47 of polar bear, 20 prosimid of rhinoceros, 20 prepollex, 306 of sarcopterygians, 38 protein sequencing, 5 of symmetrodonts, 50 Protenrec, 47 of tetrapods, 38 proteome of theropods, 9

Index 381

of triconodonts, 50 salamander, 2 of turtles, 279–80 body elongation, 143 of vertebrates, 2–4 salmon, 138, 197 Remiculus, 51 sarcopterygian, 314 reptile, 304. See Reptilia dentition body elongation, 144 replacement, 195 dentary, 224 digit homologues, 314 dentition, 177, 197, 199 pectoral fins, 137 genetic mechanisms, 186–90 relationships with other vertebrates, 38 pattern, 180 Sarcopterygii, 185 replacement, 166, 181, 186 Sauria, 339 feeding mechanism, 208 Saurichthyidae, 142 genome Saurichthys, 10, 135, 141 chromosome type, 27 body elongation, 141, 148, 159 retroelements in, 26 caudal vertebrae, 147 size of, 26 costasquamosus, 145, 150, 154 jaw closure, 221 curionii, 145, 147, 150 phalangeal formula, 353 dawaziensis, 145 sex determination of, 27 deep scales, 154 Reptilia dentition, 142 digit reduction, 346 dermal bones, 142 Rhea diversification of, 142 americana, 354 elongate jaws, 159 pennata, 354 fins rhinoceros. See Rhinocerotidae fulcra, 143 rhinoceros, woolly. See Coelodonta position, 141, 148–50, 159 antiquitatis segmentation fin rays, 143 Rhinocerotidae jaw elongation, 142, 150–2 relationships of, 20 neural crest, 151 RNA sequencing, 265 krambergeri, 145 rodent, 2, 6, 39 macrocephalus, 145, 147, 150 body size, 62 madagascariensis, 143, 154 clock-like clades, 57 male copulatory organ, 142 crown-group origin, 58 molecular mechanisms in, 135–59 dentition, 58, 186 operculum, 143 necrotic zones of limb, 348 paucitrichus, 145, 154 os falciforme, 309 scales, 142, 143, 152–8, 159 prehallux, 306 anal loop, 147 prepollex, 306 sclerotic ring, 143 presacral count, 241 somites, 145 rate of molecular evolution, 55 toxolepis, 145, 150 tarsal navicular, 306 viviparity, 142 tibiale, 307 saurischian, 25, 26 Rodentia sauropterygian, 27 thoracolumbar count, 241 Saurorhynchus brevirostris, 152 Romundina, 193 scales, deciduous, 152

382 Index

Scandentia, 39 digit reduction, 347 scapula, 9 frame shift, 343 Scarus, 124 phalangeal loss, 352 sciurid, 171 phalanx-forming region, 349 dentition, 186 sloth, giant ground, 230 Sciurus, 306 sloth, three-toed. See Bradypus Scyliorhinus canicula, 176, 179 sloth, two-toed, 347. See Choloepus seahorse, 154 snake, 241 seal dentition, 197 dentition, 186 limb reduction, 261 searobin, armoured, 154 limblessness, 301 segmentation, 143, 353 tooth replacement, 166 in Saurichthys, 145 Solenodon, 307 semaphoront, 41, 42 Somateria mollissima, 353 semilunate somites of birds, 339 in amniotes, 283 of maniraptorans, 338 in mammals, 231 sexual dichromatism in Saurichthys, 145 in parrotfish, 125 in vertebrates, 148 sexual dimorphism, 27 somitic mesoderm in limb morphology, 302 in paired appendage development, 149 sexual selection, 130 somitogenesis, 10 in parrotfish, 125 clock, 145 shark, 173 in Saurichthys, 145, 146 dental lamina, 182, 195 sonic hedgehog, 343, 348 dentition, 173, 180 Sorex, 57 fossils, 180 soricomorph, 310 pharangeal arches, 176 speciation, 20, 67, 116 scale patterning, 179 cladogenesis, 91 unpaired fins, 149, 150 in species selection, 117 shark, dogfish. See Squalus rate of, 7, 83 shark, elephant, 137 species selection, 7, 116–30 shark, Port Jackson, 169 detection of, 121–4 shrew, 57, 307, 311, 312 diversification rates, 116, 117, 118, 119, 121, dentition, 171, 224 122, 125, 126, 129 Sox9 expression, 311 estimation of, 120 shrew, North American, 317 . See Cryptotis parva extinction, 116, 117, 118, 119 Siluriformes, 152 extinction rate, 122 Simpson, G. G., 6, 91, 92, 93 measurement of, 120–1 Sinodelphys, 49 frequency of, 127–9 Sirenia group selection, 118 absence of pelves, 233 labrid fish, 124, 125, 129 sirenian. See Sirenia molecular phylogenies, 124–7 reduced lumbar count, 242 parrotfish, 127 thoracolumbar count, 243 pharyngeal mill, 125, 129 skink sexual dichromatism, 125, 127

Index 383

Price’s theorem, 117, 120, 122, 124, 129 genitalia, 313 punctuated equilibrium, 118, 124 gonadal steroids sexual selection, 125, 129 role in skeletogenesis, 313–14 speciation, 116, 117, 118, 119 Iberian mole, 310, 316, 317. See Talpa speciation rate, 122 occidentalis measurement of, 120–1 limb development, 307–16 species drift, 121 Fgf8 expression, 311 strength of, 127–9 Sox9 expression in, 310–12 Yule model, 119 Musculus abductor pollicis longus, 309 Spheniscidae, 353 Musculus palmaris longus, 309 Sphenodon, 97 os falciforme, 309, 317. See mole’s thumb punctatus, 92 acropodial origin, 314 Sphyraenia os radiale externum. See mole’s thumb barracuda, 143 prehallux, 307, 309 springhare. See Pedetes capensis prepollex, 307, 309. See mole’s thumb Squalus, 138 radial sesamoid, 314, 315. See mole’s thumb squamate, 2 sesamoid bones, 309, 315, 317 body elongation, 144 Sox9 expression, 311 limbless, 241 tibial sesamoid, 307, 313, 315, 317 3 stickleback, 138, 154 talpid mutant, 310 fins, 149 Talpidae, 307 pelvic fin, 149 Talpini, 313, 315 scales, 152 Tamandua tetradactyla, 347 stickleback, threespine, 157 Tarsipes rostratus, 212 strepsirrhine, 59 teiid lizard, 351 Struthio camelus, 338 teleost, 138, 157, 189 sturgeon. See acipenserid dental lamina, 182, 189 scutes, 153, 154 dentition, 10, 181, 190, 197 supernumerary digits. See tetrapod limb, development, 195 polydactyly tooth initiation, 190 symmetrodont, 47 fin position, 150 relationships of, 50 scale replacement, 179 synapsid, 2 Telestes, 157 axial skeleton, 240 tenrec, 47 cervical vertebrae, 245 tenrecoid, 47 differentiation of, 245 testudine, 9 hearing, 208 Testudo syndactyly, 302, 310 campanulata, 347 Syngnathidae, 154 gemoetrica, 347 graeca, 347 Taeniopygia, 27 marginata, 347 Talpa, 307, 309 Tetraodontiformes, 152 occidentalis, 310, 311, 316, 317 tetrapod, 4. See Tetrapoda Talpa occidentalis, 316 axial skeleton, 245 talpid mole, 9, 317 abaxial patterning, 245 claws, 311 dental lamina, 189

384 Index

tetrapod (cont.) os peroneium, 313 dentition, 176, 180 palmar aponeurosis. See fascia palmaris development, 178 polydactyly, 302, 305, 317 early tetrapods, 305, 314, 317 prehallux forelimbs, 138 homology, 305–7 gene knockout, 136 prepollex, 309 genome size, 26 homology, 305–7 head primary axis, 304, 314 as a morphological unit, 210 radial sesamoid, 306 jaw articulation, 207 scaphoid, 309. See tetrapod limb, carpal limb, 43 navicular development, 264, 270 sesamoid bones, 305, 309 position, 148, 149 homology of, 309 reduction, 261 tarsal navicular, 306 limbless tetrapods, 302 tarsus homology, 303 mandible, 207 tibial sesamoid, 307 as a morphological unit, 210 trapezium, 309 relationships with other vertebrates, 38 Tetrapoda, 305 stem-tetrapods, 307 thelodont. See Thelodonti tetrapod limb, 9. See also talpid mole, limb dentition, 193, 194 development pharyngeal denticle co-option, 198 acropodium, 302 pharyngeal whorls, 177 developmental patterning, 310 Thelodonti, 169, 175, 183, 193 evolutionary origin, 314 therian mammal, 38, 259 anatomy, 301 and afﬁnities of Ambondro, 49 autopodium cochlea, 41 developmental patterning, 310 diversity of, 257 evolutionary origin, 314 fossil record, 45 carpal navicular, 306 origin, 40 carpus homology, 303 premolar number, 41 development South American forms, 47 apoptosis, 310 theropod, 25, 100 mole’s thumb, 307–16 digit homology, 304 Msx expression, 310 digit reduction, 343, 351 digit homology, 303 feathers, 95 digit reduction, 351 relationship to birds, 9 diversity of, 301, 302, 303 teeth, 95 fabella, 313 Time Tree, 18 hyperphalangy, 302 Tingamarra Local fauna, 46 hypodactyly, 302 tortoise mesopodium digit reduction, 347 evolutionary origin, 314 tribospheny, 49 mineralized tendon, 305, 309 Trichechus, 234, 237 morphology, 316 absence of sacral vertebrae, 242 Musculus gastrocnemius, 313 manatus, 239 os falciforme, 306, 309 triconodont

Index 385

relationships of, 50 plastron, 9, 281, 290, 293 trout, 171 in Odontochelys, 293 trout, rainbow, 189. See Oncorhynchus mykiss pygial plates, 281 tuatara, 97 ribs, 281, 283, 293 Tuatara. See Sphenodon punctatus scapula, 280 Tulerpeton latissimus dorsi, 287 polydactyly, 305 migrating muscle precursor, 287 TUNEL, 265 pectoralis, 287 tunicate, 2 rhomboid/levator scapulae (RLS), 287 Tupaia serratus anterior (SA), 287 os falciforme, 309 scapula encapsulation, 286–90, 291, 292, 293 turtle, 4, 290, 347 somites, 285 acromion process, 280 suprapygial plates, 281 dermal armour, 280 turtle shell evolution, 290–4 embryo, 290, 293 developmental constraints, 280, 290–3 hyperphalangy, 302 tympanic ring, 207 primary axis of limb, 343 Tyrannosaurus rex, 23 relationship with pareiasaurs, 280, 283 relationships with other amniotes, 279–80, ulnare, 331, 339, 340 283 ungulate, 47, 48, 345 turtle shell, 8, 279–93 . See also Odontochelys uniformitarianism, 9 anatomy, 281 urodele axial arrest of ribs, 290, 292, 293 carpus, 330 carapace, 9, 281, 282, 283, 287, 290, 293 limb development, 270 carapacial ridge, 9, 289–90, 292, 293 Ursus spelaeus, 21 cell labelling studies, 285 costal plate origin, 283–6 vertebrate, 25, 27, 225 cell lineage labelling, 283 axial locomotion, 241 from neural crest, 285–6 axial skeleton, 8, 159, 245 in dermatome, 283, 285 comparative development, 303 in rib perichondrium, 283 dentition, 10–11 in rib periosteum, 283, 285 dermal skeletal elements, 282, 283 in sclerotome, 285 digits, 317 costal plates, 281, 282, 283 Fgf signalling, 157 dermal skeletal elements, 281, 282, 283 fossil record, 90 dermal/endochondral derivation, 281–6 genome duplication events, 138 embryo homeotic regionalization, 147 recapitulation, 291 jaws, 207 endochondral skeletal elements, 282, 283 limb development, 260 ﬂabellate ribs, 289, 290 limb patterning, 313 heterotopy, 282, 283 molecular clock, 105 intercostal muscles, 292 neural crest, 285 neural crest, 286 notochord, 292 neural plates, 281 paired appendages, 149 in Odontochelys, 282 relationships of, 2–4, 38 nuchal plates, 281 segmentation, 147

386 Index

vertebrate (cont.) skin appendage patterning, 178–80 terrestrial, 305 successional teeth, 187 tooth evolution, 10 supernumerary teeth, 187 vertebrate dentition, 166–99 tooth germs, 166, 167 acquisition from dermal skeleton, 167–9, tooth induction 173, 176–8, 193 order of, 175 acquisition from pharyngeal endoskeleton, tooth initiation, 181 167–9, 175, 176–8, 184, 193 tooth restoration in chick, 167 continuous tooth replacement, 189 vertebrate limb co-option and molecular mechanisms, Apical Ectodermal Ridge, 289 184–6 virus, 88 co-option models, 182–4 dengue, 105 dental lamina, 173, 175, 181–2, 189, 195 rate of molecular evolution, 55 dermal denticles, 173, 175, 176, 178, 179, 182, viviparity, 27 183, 184, 198 in Saurichthys, 142 patterning of, 179 dermal scales, 168 Weejasperaspis, 194, 195, 198 development of, 166 whale, 230, 257 reiterative signalling cascade, 167 dentition, 186 enamel knot, 181 early, terrestrial, 39 first dentition, 192–3 hind limb development, 268 genetic mechanisms, 186–90 hyperphalangy, 302 molecular modification of, 190–2 limb, 301 in early vertebrates, 169 reduction, 261 lungfish dentition, 196–7 Widanelfarasia bowni, 47 neural crest, 166, 177, 198 Wolffian ridge odontode, 168. See vertebrate dentition, in amniotes, 289 dermal denticles gene regulatory network, 178 Xenarthra, 47 origin, 169 xenarthran. See Xenarthran oral dentition, 192 apomorphies, 51 origin origin, 47 alternative hypotheses, 176–8 old hypotheses, 173–6 Youngolepis, 195 patterning, 177 Yule model, 119 ‘dental pattern’, 175 Yunnanolepis, 194 gene networks, 168, 169 pattern induction, 180 zalambdodonty, 47 pharyngeal denticle co-option, 198 zebra, 19 pharyngeal denticles, 168, 169, 175, 179, 183, zebra finch, 27. See Taeniopygia 192, 194, 195 zebrafish, 10, 138 pharyngeal patterning, 194–5 axial skeleton, 148 placoderm dentition, 193–4 dentition, 171, 186 placoid scales, 176, 177 pattern, 179 postbranchial lamina, 194 pharyngeal, 177, 196 region-specific tooth loss, 167 tooth initiation, 190

Index 387

tooth replacement, 189 development, 151 ﬁns, 149 scale, 153, 159, 179 pelvic ﬁns, 149 reduction, 154, 157 jaw Zone of Polarizing Activity (ZPA) articulation, 207 polydactyly, 310, 313