EVOLUTION—THE EXTENDED SYNTHESIS edited by Massimo Pigliucci and Gerd B. Müller The MIT Press Cambridge, Massachusetts London, England © 2010 Massachusetts Institute of Technology All rights reserved. No part of this book may be reproduced in any form by any electronic or mechanical means (including photocopying, recording, or information storage and retrieval) without permission in writing from the publisher. MIT Press books may be purchased at special quantity discounts for business or sales promotional use. For information, please email [email protected] or write to Special Sales Department, The MIT Press, 55 Hayward Street, Cambridge, MA 02142. This book was set in Times Roman by Toppan Best-set Premedia Limited. Printed and bound in the United States of America. Library of Congress Cataloging-in-Publication Data Evolution—the extended synthesis / edited by Massimo Pigliucci and Gerd B. Müller. p. cm. Includes bibliographical references and index. ISBN 978-0-262-51367-8 (pbk. : alk. paper) 1. Evolution (Biology) 2. Evolutionary genetics. 3. Developmental biology. I. Pigliucci, Massimo, 1964– II. Müller, Gerd B. QH366.2.E8627 2010 576.8—dc22 2009024587 10 9 8 7 6 5 4 3 2 1 Index Abir-Am, Pnina, 445 Average effects, 87 Abstract gene model, 102 Avital, E., 165 Accommodation, 298, 324, 366. See also Phenotypic and genetic Badyaev, A. V., 365 accommodation Baldwin effect, 219, 257–258, 366, 367, Activator-inhibitor systems, 290 371 Adams, Paul, 220 Baldwin, James Marc, 219, 366, 367, 371 Adaptation, 163–164, 425–427 Bat wings, 268 Adaptation and Natural Selection Beaks, fi nch, 271 (Williams), 84, 88 Behavioral inheritance, 187 Adaptive cell behaviors, 268 Benkemoun, L., 153–154 Adaptive landscapes/adaptive Biodiversity, areas for future research on topographies. See Fitness landscapes origins of, 65–71 Adaptive radiation Bioeconomics, 469–470 defi ned, 65 Biogenetic law, Haeckel’s, 257 theory of, 65–68 “Biological” species concept, 8 Adaptive solutions, multiple, 33–34 Biologists, entrenched separation between Adhesion (ADH), 286f, 287 evolutionary and developmental, 394 Agents, 220 Biology Allee, W. C., 83 evolutionary, 8 Alligator mississippiensis, 320f integrative, 365 Allopatric speciation, 8 Biotechnology, 381 Allostery, 265 “Bipedal goat effect,” 362, 369 “Altenberg 16,” vii–viii Bipedal macque, 369, 370f Altruism, 85–87 “Blending of inheritance,” 5 Anatomical variation, nature of, Blount, Z. D., 38 271 Bone-forming cells, 268 Animal diversity, burst of Bone morphogenetic protein 4 (BMP4), during Cambrian radiation, 336 271 Anthropology, evolutionary, 91 Boogerd, F. C., 471 Anti-reductionist consensus, 461–464 Botany. See also Plants Antlers, 273–274 Modern Synthesis and, 8 Apical-basal (A/B) polarity (POL), Brain, 69 induction of, 288–289 how fi tness is defi ned in the, 237–238 Arabidopsis thaliana, 122–123, 126–129, size and complexity, 69 356f, 362, 363f Brighton, Henry, 240 Arch-back nursing (ABN), 161–162 Brooks, D. R., 446 Area effect, 67 Buffering, 357–361 Arthur, Wallace, 423, 424f Ashby, W. R., 192 Calvin, W. H., 221 Aunger, Robert, 220 Cambrian explosion, 336, 337f, 338–339 Autocatalysis, 210–212, 212f Canalization, 140–141, 357–360 486 Index Capacitance, 360–361 Connected components, defi ned, 55 Carroll, Sean B., 407 Conserved genes and core processes for Cartwright, Nancy, 466 evolution, 256, 259–261 Causal-mechanistic approach, shift Consilience, 474n2 toward, 12–14 Consilience (Wilson), 446 CBF-1-Su(H)-Lag-1 (CSL), 287 Constraining principles, 427 Cecciarelli, L., 447, 448 Constraint, 394–395 Cell differentiation, 281 defi ned, 394 Cell heredity, 141 Control webs, 197, 202 Cell learning through epigenetic Cooperative behavior, 85, 86, 201 inheritance, 156–157, 156f Correlation vs. causation, emphasis on, Cell memory, 141 12 Cellular epigenetic inheritance, 144–152 Culture, evolutionary perspective on, Cellular epigenetic learning, 156–157, 91–92 156f Cytosines, methylation and demethylation Cellular epigenetic variants of, 142–143, 147. See also Methylation prevalence, stability, and induction of, marks 152–153 Cellular epigenetic variation, transmission Darden, Lindley, 444, 445 of developmentally induced, 144–152 Darwin, Charles. See also specifi c topics Cellular epigenetics, expanding the scope on direction-giving and creative role of of studies of, 156–157 natural selection, 22 Cerebral capacity, 69–70 Fleeming Jenkin and, 29 Cervical vertebrae, 268 hallmark of his theory of evolution, 298 Chance variation(s), 21, 33–39. See also as integrator of information, 97 Divergence, evolutionary; Variation invention and subordination of chance Darwin’s invention and subordination of, variation, 22–29 22–29 mechanism of evolution, 295, 297, 298 importance, 39–42 on relationship between theory and vs. natural selection, 21, 41–42 “data,” 373 natural selection of, 21 Darwinism subordination throughout evolutionary essence, 21–22, 33 synthesis, 30–33 ideas underlying the original, 5 Changeux, J.-P., 217 key concepts, 11f Charlesworth, Brian, 269, 270 period of “eclipse,” 5 “Cheating,” 201 vs. selectionism, 219 Chemical origin of evolvability and Dawkins, Richard, 32–33 systems chemistry in statu nascendi, Deer antlers, 273–274 210–214 Demethylation of cytosines, 142 Chetverikov, Sergei, 31 Development Chromatin marking, epigenetic epigenetic inheritance and evolution of, inheritance through, 147–150 166 Ciliates, 147 evolution and, 394–395 Citrate metabolism, 37 Developmental biology, 8, 299. See also Cnidaria, 283 Evolutionary developmental biology Codon-based gene model, 104 Developmental-genetic tool kit, 283, 284 Cognition, neuronal replicators in, Developmental genetics, 269, 270 214–216 Developmental networks, 139 Cognitive explosion phase, 70–71 Developmental regulatory networks, 324. Coin problem. See 10-coin problem See also Gene regulatory networks Common descent of all living organisms, Differential adhesion (DAD), 286f, 287 5 Differentiated states, inheritance of, 142 Commoner, Barry, 457 Differentiation, systems that control, Communicative niche construction, 186 142 Communities as targets of selection, 138, Digit reductions and additions, 319–320, 139 320f, 321f, 322 Compartmentation, 267–269, 272, 273 Diploblasts, 283–284 Competition between groups, 82, 83 Dirac, Paul, 459–460 Index 487 Directed variation, 22, 42 Epigenetic approaches to evolutionary vs. chance variation, 22 (see also Chance change, 140–141 variation(s)) Epigenetic control systems, 141–143 Disease transmission, 161 Epigenetic inheritance, 141–144, 187. See Divergence, evolutionary, 138. See also also Cellular epigenetic inheritance; Chance variation(s) Soma-to-soma transmission Diversity. See Biodiversity defi ned, 187 DNA, 9, 138–139, 457. See also Chromatin evolutionary implications, 163–168 marking Epigenetic inheritance systems (EISs), DNA modifi cation, 142 145, 152, 153 DNA sequences, 99 types of, 145–152 Dobzhansky, Thoedosius, 6–7, 31, 41, 42, Epigenetic innovation, 307, 308. See also 91, 278, 412–413, 474n3 Variation-innovation distinction Downward causation, 460–461 environmental factors and, 315 Dresden, M., 461 Epigenetic innovation theory, 322–327 Drosophila sp., 31, 141, 142 key components, 322–323 D. Pseudoobscura, 32 Epigenetic integration, 315 Dupré, John, 466 Epigenetic learning, 156–157, 156f Dynamical interactions in development, Epigenetic research, areas of, 140–141 316, 317f Epigenetic traps, 324 Dynamical patterning modules (DPMs), Epigenetic turn, 140–145 285, 297–300 Epigenetic variation(s). See also Cellular metazoan forms generated by, 293, 294f epigenetic variants molecules, physics, and outcomes of the direct and indirect induction of, 155, major, 285–293 155f names, components, and roles in inheritance of acquired, 143 evolution and development of modes of transmission, 144, 145f metazoan, 285–286, 286t transmission of developmentally induced cellular, 144–152 Ecological inheritance, 176, 180–181, Epigenetics, 144. See also Cellular 186–187 epigenetics vs. genetic inheritance, 181 development, genetics, and, 362–365 informational, 197–201 Epigenome, evolutionary potential of, physical, 193–197 127–129 types of, 187, 189 Epistasis, genome networks and, 124–127 Ecological niches, 158. See also Niche Epithelial-mesenchymal transformation, construction 293 dynamics of invasion of empty, 67–68 Epitheliod tissue, 292 Ecology, 469 Error correction (EC) mechanisms, 224f evolutionary, 8 Escherichia coli (E. coli), 34–37, 36f, 37 Modern Synthesis and, 8 Eukaryotes, 9, 260 Ecosystem engineering, 178, 194–196, 202 Eukaryotic cell, 88, 167 Edelman, G. M., 217, 218 Eumetazoa, 283–284 Eigen’s replicating equation, 221 EvoDevo. See Evolutionary Elk antlers, 273–274 developmental biology Embryo, spatial compartments in, 267–268 Evolution. See also specifi c topics Embryology, 8 Darwin’s mechanism of, 295, 297, 298 Embryonic induction, 266 defi nitions, 454 Emergentism, 461 theory of Engineering webs, 197, 202 hallmark of Darwin’s, 298 Environment and developing phenotype, principles underlying, 276 362 units of, 209, 220 Environmental factors and innovation, Evolution (Barton), 419, 421 315 Evolution (Huxley), 449 Environmental induction, 315–316 Evolution (Ridley), 419, 420–421t Environmentally mediated genotypic Evolution textbooks, 423, 425. See also associations (EMGAs), 197, 202 under Evolutionary theory, broad Epiallele formation, 129 representations of 488 Index Evolutionary and physiological variation, extended synthesis, unifi cation, and 275 coherence, 433–434 (see also Extended Evolutionary Biology/Evolution