HISTORICAL BIOGEOGRAPHY JORGE V CRISCI LILIANA KATINAS PAULA POSADAS HISTORICAL BIOGEOGRAPHY AN INTRODUCTION HARVARD UNIVERSITY PRESS Cambridge, Massachusetts London, England 2003 Copyright © 2003 by the President and Fellows of Harvard College All rights reserved Printed in the United States of America Library of Congress Cataloging-in-Publication Data Crisci, Jorge Victor Historical biogeography : an introduction / Jorge V Crisci, Liliana Katinas, Paula Posadas p cm Includes bibliographical references and index ISBN 0-674-01059-0 (cloth : alk paper) Biogeography—History I Katinas, Liliana II Posadas, Paula III Title QH84 C6798 2003 578′.09—dc21 2002192236 PREFACE In a 1959 essay entitled “The Voice of Poetry in the Conversation of Mankind,” Michael Oakeshott develops the notion of knowledge as a community-owned social construct that is the result of our ability to participate in an unending conversation Oakeshott says: “As civilized human beings, we are the inheritors, neither of an inquiry about ourselves and the world, nor of an accumulating body of information, but of a conversation, begun in the primeval forests and made more articulate in the course of centuries It is a conversation which goes on both in public and within each of ourselves.” According to Oakeshott, education, properly speaking, is an initiation into the skills and partnership of this conversation in which we learn to recognize the voices, to distinguish the proper occasions of utterance, and in which we acquire the intellectual and moral habits appropriate to conversation And it is this conversation that, in the end, characterizes every human activity and utterance Each voice reflects a human activity, begun without premonition of where it would lead, but acquiring for itself in the course of the engage- v vi Preface ment a specific personality and manner of speaking Over time, each voice modulates in reaction to those around it Among the voices of biology, historical biogeography recently has acquired, or begun to acquire, an authentic voice and language of its own Our purpose is to consider the voice of historical biogeography: its utterances, manners of speaking, modulation, and manner of thinking, which in this book are influenced strongly by histories of South America To listen to the voice of historical biogeography using empirical examples from South America is to return to the birth of evolutionary theory Darwin himself stated in the opening paragraph of The Origin of the Species (1859): “When on board H.M.S Beagle, as naturalist, I was much struck with certain facts in the distribution of the inhabitants of South America, and in the geological relations of the present to the past inhabitants of that continent These facts seemed to me to throw some light on the origin of species.” Today, as in Darwin’s time, the distribution of living beings offers an inexhaustible source of light on the evolution of life on Earth There are few facets of evolutionary biology that cannot be illuminated by the study of the history of these distributions, otherwise known as historical biogeography Furthermore, historical biogeography is passing through an extraordinary revolution encompassing its fundamental principles, basic concepts, methods, and relationships with other disciplines of comparative biology In this book we explain and illustrate the fundamentals and the most frequently used methods of historical biogeography, including how to recognize when one has a research problem that requires a historical biogeographic approach; how to decide upon the most appropriate kind of data to collect; how to choose the best method for the problem at hand; how to perform the necessary calculations, and if a computer program is needed, which one to use; and how to interpret the results It is not our goal to suggest the adoption of a single method, but to elucidate the biological assumptions of each method We include case studies, selected mainly from our own research Preface These studies encompass a variety of research goals and contexts and give an overall impression of how these methodologies are used Although this book is primarily a text for researchers and students of biology, it may also interest those in such fields as geology and geography, since the voice of historical biogeography echoes in many sciences We would like to thank A Bartoli, M Bonifacino, M Donato, M Ebach, M Heads, P Hoch, P Ladiges, D Miranda-Esquivel, G Nelson, F Ocampo, E Ortiz Jaureguizar, J Patton, S Roig-Juñent, R Tortosa, and G Voelker for comments on the manuscript or parts of the manuscript We greatly appreciate Piero Marchionni and Mariano Donato’s help in the preparation of this book We would like to acknowledge the invaluable help of Lucy Gómez de Mainer who spent a lot of her time improving our English Hugo Calvetti prepared the illustrations for this book We would also like to thank our editor, Michael Fisher, and our manuscript editor, Kate Brick, for encouragement and professional assistance The advice of Brian Farrell, Gary Nelson, Jim Wilgenbusch, and one anonymous reviewer have undoubtedly made this book of much higher quality that it would have been otherwise Those faults that still remain are entirely our responsibility Our research on biogeography was supported by National Geographic Society (Grants #3966–88, 4662–91, 5776–96); Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Argentina; and Agencia Nacional de Promoción Científica y Tecnológica (PICT99 N 6866) Permission to reprint an excerpt by Jorge Luis Borges from “Avatars of the Tortoise,” in Labyrinths, copyright © 1962, 1964, has been granted by New Directions Publishing Corporation Finally, Victoria Crisci, Elena Katinas, and Edgardo Ortiz Jaureguizar have assisted us and supported us throughout this project We may never be able to repay them for all their help, encouragement, and extraordinary patience vii CONTENTS Introduction: What Is Historical Biogeography? I METHODS IN HISTORICAL BIOGEOGRAPHY 19 Distribution Areas and Areas of Endemism Center of Origin and Dispersal 30 Phylogenetic Biogeography Ancestral Areas 42 Panbiogeography 53 21 37 Cladistic Biogeography 67 Parsimony Analysis of Endemicity 10 11 86 Event-Based Methods 100 Phylogeography 118 Experimental Biogeography 127 A Comparison of Methods: The Case of the Southern Beeches 132 ix 236 Works Cited Smith, A B 1992 Echinoid distribution in the Cenomanian: An analytical study in biogeography Palaeogeog Palaeoclimatol Palaeoecol 92:263–276 Soulé, M E 1991 Conservation: Tactics for a constant crisis Science 253:744–750 Spellerberg, I F and J W D Sawyer 1999 An Introduction to Applied Biogeography Cambridge: Cambridge University Press Stheli, F G and S D Webb (eds.) 1985 The Great American Biotic Interchange New York and London: Plenum Press Stuessy, T F., T Sang, and M L De Vore 1996 Phylogeny and biogeography of the subfamily Barnadesioideae with implications for early evolution of the Compositae In Compositae: Systematics Proceedings of the International Compositae Conference Kew, 1994, D J N Hind and H J Beentje (eds.) Royal Botanical Gardens Kew, Vol 1, pp 463–490 Sun, H., W McLewin, and M F Fay 2001 Molecular phylogeny of Helleborus (Ranunculaceae), with an emphasis on the East Asian–Mediterranean disjunction Taxon 50:1001–1018 Swenson, U., A Backlund, S McLoughlin, and R S Hill 2001 Nothofagus biogeography revisited with special emphasis on the enigmatic distribution of subgenus Brassospora in New Caledonia Cladistics 17:28–47 Swenson, U and K Bremer 1998 Pacific biogeography of the Asteraceae genus Abrotanella (Senecioneae, Blemnospermatinae) Syst Bot 22:493–508 Swenson, U and R S Hill 2001 Most parsimonious areagrams versus fossils: The case of Nothofagus (Nothofagaceae) Aust J Bot 49:367–376 Swenson, U., R S Hill, and S McLoughlin 2000 Ancestral area analysis of Nothofagus (Nothofagaceae) Aust Syst Bot 13:469–478 Swofford, D L 2000 PAUP* (Phylogenetic Analysis Using Parsimony and other methods) Sunderland, Mass.: Sinauer Swofford, D L., G J Olsen, P J Waddell, and D M Hillis 1996 Phylogenetic inference In Molecular Systematics, 2nd Ed., D M Hillis, C Moritz, and B K Mable (eds.) Sunderland, Mass.: Sinauer, pp 407–514 Swofford, D L., P J Waddel, J P Huelsenbeck, P G Foster, P O Lewis, and J S Rogers 2001 Bias in phylogenetic estimation and its relevance to the choice between parsimony and likelihood methods Syst Biol 50:525–539 Takezaki, N., A Rzhetsky, and M Nei 1995 Phylogenetic test of the molecular clock and linearized trees Molec Biol Evol 12:823–833 (the computer program Lintre is available from http://www.cib.nig.ac.jp/dda/ntakezak/ ntakezak.html) Takhtajan, A 1986 Floristic Regions of the World Berkeley: University California Press Works Cited Templeton, A R 1998 Nested clade analysis of phylogeographic data: Testing hypotheses about gene flow and population history Mol Ecol 7:381–398 ——— 2001 Using phylogeographic analyses of gene trees to test species status and processes Mol Ecol 10:779–791 Templeton, A R., E Routman, and C A Phillips 1995 Separating population structure from population history: A cladistic analysis of the geographical distribution of mitochondrial DNA haplotypes in the Tiger salamander, Ambystoma tigrinum Genetics 140:767–782 Trejo-Torres, J C and J D Ackerman 2001 Biogeography of the Antillas based on a parsimony analysis of orchid ditributions J Biogeog 28:775–794 Tuffley, C and M A Steel 1997 Links between maximum likelihood and maximum parsimony under a simple model of site substitution Bull Math Biol 59:581–607 Udvardy, M D F 1969 Dynamic Zoogeography with Special Reference to Land Animals New York: Van Nostrand Reinhold Ulfstrand, S 1992 Biodiversity – How to reduce its decline Oikos 63:3–5 Vander Zanden, M J., J M Casselman, and J B Rasmussen 1999 Stable isotope for the food web consequences of species invasions in lakes Nature 401:464– 467 Vane-Wright, R I., C J Humphries, and P H Williams 1991 What to protect? – Systematics and the agony of choice Biol Conserv 55:235–254 Van Steenis, C G G J 1962 The land-bridge theory in botany with particular reference to tropical plants Blumea 11:235–542 Van Steenis, C G G J 1971 Nothofagus, key genus of plant geography, in time and space, living and fossil, ecology and phylogeny Blumea 19:65–98 van Veller, M G P and D R Brooks 2001 When simplicity is not parsimonious: A priori and a posteriori methods in historical biogeography J Biogeog 28:1–11 van Veller, M G P., D J Kornet, and M Zandee 2000 Methods in vicariance biogeography: Assessment of the implementation of assumptions 0, 1, and Cladistics 16:319–345 van Veller, M G P., M Zandee, and D J Kornet 1999 Two requirements for obtaining valid common patterns under different assumptions in vicariance biogeography Cladistics 15:393–406 Vinnersten, A and K Bremer 2001 Age and biogeography of major clades in Liliales Amer J Bot 88:1695–1703 Vitousek, P., H A Mooney, J Lubchenco, and J M Melillo 1997 Human domination of Earth’s ecosystems Science 277:494–499 237 238 Works Cited Voelker, G 1999a Dispersal, vicariance, and clocks: Historical biogeography and speciation in a cosmopolitan Passerine genus (Anthus: Motacillidae) Evolution 53:1536–1552 ——— 1999b Molecular evolutionary relationships in the avian genus Anthus (Pipits: Motacillidae) Mol Phylogenet Evol 11:84–94 Walker, D E and J C Avise 1998 Principles of phylogeography as illustrated by freshwater and terrestrial turtles in the southeastern United States Annu Rev Ecol Syst 29:23–58 Wallace, A R 1876 The Geographical Distribution of Animals New York: Hafner ——— 1892 Island Life London: Macmillan Waters, J M., J A López, and G P Wallis 2000 Molecular phylogenetics and biogeography of Galaxiid fishes (Osteichtyes: Galaxiidae): Dispersal, vicariance, and the position of Lepidogalaxias salamandroides Syst Biol 49:777–795 Wegener, A 1915 Die Entstehung der Kontinente und Ozeane Braunschweig: Vieweg & Sohn Weston, P and M D Crisp 1994 Cladistic biogeography of the Waraths (Proteaceae: Embothrieae) and their allies accross the Pacific Aust Syst Bot 7:225–249 ——— 1996 Trans-Pacific biogeographic patterns in the Proteaceae In The Origin and Evolution of Pacific Islands Biotas, New Guinea to Polinesia: Patterns and Processes, A Keast and S E Miller (eds.) Amsterdam: Academic Publishing, pp 215–232 Wiley, E O 1980 Phylogenetic systematics and vicariance biogeography Syst Bot 5:194–220 ——— 1981 Phylogenetics: The Theory and Practice of Phylogenetic Systematics New York: Wiley-Intersci ——— 1987 Methods in vicariance biogeography In Systematics and Evolution: A Matter of Diversity, P Hovenkamp (ed.) Utrecht: Institute of Systematic Botany, Utrecht University, pp 283–306 ——— 1988 Vicariance biogeography Annu Rev Ecol Syst 19:513–542 Williams, W T and M B Dale 1965 Fundamental problems in numerical taxonomy Adv Bot Res 2:35–68 Wilson, R J 1983 Introducción a la Teoría de Grafos Madrid: Alianza Editorial Wolfe, K H 1991 Mammalian DNA replication: Mutation biases and the mutation rate J Theor Biol 149:441–451 Xiang, Q Y., S J Brunsfeld, D E Soltis, and P S Soltis 1996 Phylogenetic relationships in Cornus based on chloroplast DNA restriction sites: Implications for biogeography and character evolution Syst Bot 21:515–534 Works Cited Xiang, Q Y., D J Crawford, A D Wolfe, Y C Tang, and C W DePamphilis 1998 Origin and biogeography of Aesculus L (Hippocastanaceae): A molecular phylogenetic perspective Evolution 52:988–997 Yang, Z H and B Rannala 1997 Bayesian phylogenetic inference using DNA sequences: A Markov Chain Monte Carlo method Mol Biol Evol 14:717–724 Zandee, M and M C Roos 1987 Component-compatibility in historical biogeography Cladistics 3:305–332 Zink, R M 1996 Comparative phylogeography in North American birds Evolution 50:308–317 Zink, R M., R C Blackwell-Rago, and F Ronquist 2000 The shifting roles of dispersal and vicariance in biogeography Proc R Soc Lond B 267:497–503 Zuckerkandl, E and L Pauling 1962 Molecular disease, evolution, and genetic heterogeneity In Horizons in Biochemistry, M Kasha and B Pullman (eds.) London and New York: Academic Press, pp 189–225 ——— 1965 Evolutionary divergence and convergence In Evolving Genes and Proteins, V Bryson and H J Vogel (eds.) London and New York: Academic Press, pp 97–166 Zunino, M 2000 El concepto de área de distribución: Algunas reflexiones teóricas In Hacia un Proyecto CYTED para el Inventario y Estimación de la Diversidad Entomológica en Iberoamérica: PrIBES 2000, F M Piera, J J Morrone, and A Melic (eds.), vol Zaragoza: SEA, Monografías Tercer Milenio, pp 80–85 Zunino, M and A Zullini 1995 Biogeografía: La Dimensione Spaziale dell’Evoluzione Milan: Casa Editrice Ambrosiana 239 INDEX Page numbers in bold indicate figures or tables Aares, E., 126 Absent areas, 68–71 Ackerman, J D., 99 Africa, 41, 157–158 Aguilar-Aguilar, R., 66 Alcántara, O., 99 Alroy, J., 58 Amazonia, 124–126 America, 34, 66, 85, 117 Ancestral areas, 14, 17; definition, 11; main characteristics, 15–16; and phylogenetic biogeography, 39; assumptions, 42; Camin-Sokal optimization, 43–45, 44; criticisms, 45, 49; Fitch optimization, 45–47, 46; weighted ancestral area analysis, 47– 49; case study, 49–50, 51; research using, 52; applied to Nothofagus, 138–139; and molecular data, 153; applied to Anthus, 157–158 Ancestral species map, 17 Andean subregion, 61–63, 92–96, 114–116, 168 240 Anderson, W W., 157 Andersson, L., 10 Andes orogeny, 50, 63, 66 Animals, by taxonomic genus See Invertebrates; Vertebrates Anophelinae, 159 Antarctica, 135–139 Area biogeography, 9, 138, 142–146, 148 Area cladograms, 12; constructing of, 68–71; assumptions (0, 1, and 2), 68–71, 70 Areagrams, 139 Areas of endemism: definition, 25–26; overlapping of distribution areas, 26; area quadrating methods, 26; delimitation problems, 27–28; size, 28; optimality criteria, 28 Areographic methods, 22 Artigas, J N., 26 Assumptions (0, 1, and 2), 68–71, 70 Asteraceae, 63–66 Auckland Islands, 66 Australasia, 39 Index Australia, 28, 41, 61–62, 82–85, 117, 132–134, 138–146, 157–158, 179 Avise, J C., 5, 13, 17, 118, 120, 121, 124, 126, 167, 168, 188 Axelius, B., 23 Axelrod, D I., 31, 135, 136 Balanced biogeography See Experimental biogeography Baldwin, B G., 159 Ball, I R., 147 Baseline, 56, 57 Bates, J M., 99 Bayesian approach to cospeciation, 17; definition, 111–112 Bayesian methods: in coevolutionary studies, 111–112; and molecular clocks, 156; in phylogenetic inference, 192 Beyra, M A., 117, 153 Biodiversity: definition, 1; and conservation, 91, 161–166; and global changes, 160, 174–175; atlas, 166; and biogeography methods, 166–168; case studies, 168–173 Biogeographic homology, 57, 166 See also Spatial homology Biogeographic hypothesis See Hypotheses in historical biogeography Biogeographic synapomorphies, 87 Biogeography: definition, 1–2; historical biogeography, 2, 4–5, 128; ecological biogeography, 2, 128; biologist´s perception of, 3–4; stochastic biogeography, 128; balanced biogeography, 128; molecular biogeography, 152 Biological diversity, conservation, 160–173 See also Biodiversity Biological invasions: characteristics, 176– 177; consequences, 178–179 Biotic exchanges, 160, 174–175 See also Species introduction Biotic homogenization, 178–179 Bisconti, M., 99 Blake, R D., 156 BPA See Brooks parsimony analysis Bremer, K., 11, 17, 23, 42, 43, 45, 46, 47, 48, 49, 52, 108, 117, 138, 157, 158 Brooks, D R., 72, 75, 77, 85, 127 Brooks parsimony analysis, 17; definition, 72, 74, 76; primary BPA, 72–75; secondary BPA, 75; criticisms, 77; case studies, 83, 97, 114–116; misuse in PAE, 92 Brown, G K., 85, 153 Brown, J H., 161, 174, 175, 176, 177, 178 Brown, J M., 126, 153 Brundin, L., 11, 17, 37, 39, 40, 41, 134 Cabrera, A L., 27, 50, 95, 96, 114 Caccone, A., 152, 159 Cadle, J E., 127 Cain, S A., 7, 22, 31, 32 Cambefort, Y., 85 Camin-Sokal optimization: and ancestral areas, 43–45; and phylogenetic reconstruction, 188 Canary Islands, 157–158, 159 Candolle, A P de, 2, 23 Carabid beetles, 39–40 Carpenter, J M., 82 Cartographic methods, 22 Cavalli-Sforza, L L., 189 Cavieres, L A., 167 Center of origin and dispersal, 14, 17; definition, 11; main characteristics, 15–17; principles, 31; criteria, 32; criticisms, 33; and molecular clock, 33–34; case study, 34; and phylogenetic biogeography, 37, 38, 39; and ancestral areas, 42, 47; and panbiogeography, 57 Central America, 85 Central Chile, 55, 61, 62, 65, 95, 96, 114–116 Chanderbali, A S., 159 Chapco, W., 126 Characters: plesiomorphous, 186; apomorphous, 186; morphological, 188; molecular, 188 Charleston, M A., 17, 101, 111 Chatham Islands, 66 Chile, 49, 55, 61, 85 Chloroplast DNA See DNA 241 242 Index Choosing methods in biogeography, 146– 148 Chronobiogeographical paradigm, 153 Cifelli, R L., 36 Clade distance, 124 Cladistic biogeography, 14; definition, 12, 67–68; main characteristics, 15–17; area cladograms construction, 68–71; assumptions (0, 1, and 2), 68–71, 70; component analysis, 71–72, 73; Brooks parsimony analysis, 72–77, 74, 76; three-area statements, 77, 78; paralogy-free subtrees, 78– 81, 80; integrative method, 81; comparing methods, 82; case studies, 82–85, 96–99; research using, 85; using Nothofagus, 142– 144; software, 196 Cladistic nested analysis See Nested clade analysis Cladistics, 185–189 See also Phylogenetic reconstruction Classical biogeography See Experimental biogeography Climo, F M., 66 Cliques, in panbiogeography, 59 Coalescence time, 154 Codivergence See Historical associations Coevolution See Event-based methods Coevolutionary two-dimensional cost matrix, 17 Colonists, 176, 177 Colonization, 102 Combined method, 17; definition, 112–113; case study, 114–116 Comparison of methods: in cladistic biogeography, 82; in historical biogeography, 132–148 Complementarity, 162–166 Component analysis, 17; definition, 71–72, 73; case studies, 82–85, 96–99 Component compatibility, 17 Computer programs: PHYLIP, 60, 72, 125, 195, 199, 200; SECANT, 60, 64, 195; CLINCH, 60; COMPONENT (1.5), 72, 97, 196; Hennig86, 72, 87, 90, 94, 97, 115, 144, 170, 198, 200; PAUP, 72, 87, 90, 125, 199, 200; NONA, 72, 90, 94, 198, 200; TASS, 77, 79, 81, 97, 144, 196; TAS, 77, 81, 97, 196; COMPONENT (2.0), 104, 115, 139, 144, 197; DIVA, 109, 115, 197; Geo-Dis, 124, 198; CAFCA, 196; TreeMap, 197; TreeFitter, 197; Pee-Wee, 199; TNT, 199, 200; MrBayes, 200; Bambe, 201; Winclada, 201; TreeView, 201; MacClade, 202; r8s, 202 Concave function, 48 Condie, K C., Connor, E F., 54, 58 Conran, J G., 99 Conservation, phylogenetic measures for, 164 See also Biodiversity Constrained DIVA, 109, 110 Continuous track analysis, 58 Contreras-Medina, R., 66 Coscarón, M del C., 99 Cospeciation, 102 Couper, R A., 136 Cox, C B., 2, Cracraft, J., 89, 92 Craw, R C., 5, 6, 9, 12, 17, 33, 53, 54, 58, 59, 60, 64, 66, 82, 86, 88, 89, 92, 134, 135, 138, 146, 162, 166, 181 Creobina, 62 Crisci, J V., 2, 3, 4, 11, 17, 25, 26, 49, 54, 60, 61, 64, 68, 81, 83, 85, 92, 134, 138, 142, 143, 148, 160, 167, 168, 181, 182, 185, 186, 189, 194 Crisp, M D., 18, 27, 85, 134, 136, 138, 143, 144 Croizat, L., 1, 3, 7, 9, 11, 17, 33, 53, 54, 68, 134 Croizer, R H., 164, 167 Crustal evolution, Cruzan, M B., 121 CTA See Continuous track analysis Cuvier, G., 185 Cynipoid wasps, 117 Dale, M B., 114 Darlington, P J., Jr., 31, 39, 132, 135, 136 Darwin, C., 30, 135, 185 Index da Silva, M N F., 124, 126 Davis, C C., 159 Dawson, M N., 126 Deep coalescence, 102 De Meyer, M., 85 Desalle, R., 159 Dettman, M E., 135, 136 Deviation rule, 38 See also Phylogenetic biogeography Diamesinae, 83 di Castri, F., 174 Dispersal, 6, 7, 8, 14, 15, 101, 102, 103, 109, 129, 130; predicted dispersal, 7, 110; random dispersal, 7, 110; geodispersal, 7–8, 76; as parallelisms, 89, 109–110; and species introduction, 175 Dispersalism See Center of origin and dispersal Dispersal-vicariance analysis, 17; definition, 108–111; case study, 114–117; applied to Nothofagus, 140–142; applied to Anthus, 157–158 Distance methods See Phylogenetic reconstruction Distribution areas, 22 DIVA See Dispersal-vicariance analysis DNA, 151, 188–189; mtDNA, 13, 118–120, 125, 154, 156–157; cpDNA, 13, 120 Domínguez, E., 85 Donoghue, M J., 153 Dowd, J M., 134, 136 Drosophilidae, 159 Duplication events, 103, 104, 109, 110 See also Geographic paralogy Ebach, M C., 11, 49 Ebenhard, T., 179 Echymidae, 124, 126 Edentata, 35 Edgecombe, G D., 11 Edwards, A W F., 189 Eldredge, N., 75 Eliosa, H., 66 Ellsworth, D L., 126 Emerson, B C., 99 Endemicity in conservation, 164–166 Endemism, areas of See Areas of endemism Enghoff, H., 17 Engler, A., 134 ESU See Evolutionary significant units Eurasia, 157–158, 159 Event-based methods, 14, 17; definition, 12, 100–101; main characteristics, 15–17; reconciled trees, 101, 104, 106–108, 107; dispersal-vicariance analysis, 108–111; jungles, 111; bayesian approach to cospeciation, 111–112; combined method, 112–113; metricity, 113–114; case study, 114–116; research using, 117; applied to Nothofagus, 139–142, 144–145; and molecular data, 153; software, 197 Evolutionary significant units, 167–168 Ewel, J J., 175, 178, 179 Exclusion, 102 Exotic species, 176–179 Experimental biogeography, 14, 17; definition, 13, 127–128; main characteristics, 15–17; biogeographic model, 128–131 Extensionists, 31 Extinction, 6, 14, 15, 102, 104, 105, 109–110, 129, 130, 164; as reversions, 89; and species introduction, 175 Ezcurra, C., 52 Fairbrothers, D E., 135 Faith, D P., 164 Farrel, B D., 156 Farris, J S., 72, 188, 198 Felidae, 36 Felsenstein, J., 60, 72, 123, 189, 191, 195 Fiala, K., 60 Fitch, W M., 76 Fitch optimization: and ancestral areas, 17, 45–47; and phylogenetic reconstruction, 188 Florin, R., 136 Forbes, E., 31 Forey, P L., 39 Fos, M., 156 Francisco-Ortega, J., 159 243 244 Index Franco, P., 66 Frenguelli, J., 64 Fritsch, P., 52, 117, 159 Fujii, N., 126 Fungi: Cyttaria, 62, 83, 144; Lentinula, 159 Galaxiid fishes, 159 García-Barros, E., 99 Gatrell, A., Gene duplication, 102 Gene loss, 102 Gene transfer, 102 Genealogical concordance, 121, 122, 123, 125 Generalized tracks, 11, 57 Geodispersal See Dispersal Geographic paralogy, 9, 10, 78, 101, 102, 103 Geographic synapomorphies See Biogeographic synapomorphies Gibraltar Strait, 85 Giller, P S., Gillespie, J H., 154 Glaciations, 50, 63, 66, 126, 158 Global tectonics, See also Crustal evolution Goloboff, P A., 72, 198, 199 Gondwana, 57, 63, 132–134, 142–146, 159 Great American Biotic Interchange, 34–36 Greene, H W., 127 Grehan, J R., 33, 54, 57, 66, 161, 162, 167 Hadju, E., 66, 85 Haeckel, E., 185 Hahn, W J., 159 Hall, B G., 192 Hanks, S L., 135 Haraway, D J., Harold, A S., 25, 26, 28 Harrison, R G., 126 Harvey, P H., 151 Hausdorf, B., 17, 25, 47, 48, 49, 52, 138 Hawaiian Islands, 85, 159, 178, 179 Haydon, D T., 13, 17, 127, 181 Hayes, J P., 126 Heads, M J., 23, 53, 57, 66, 167 Heard, S B., 164 Heisenberg, W., Helfgott, D M., 159 Henderson, I M., 23, 25, 54 Hennig, W., 37, 68, 185 Hesse, M., Heywood, V H., 133 Hibbett, D S., 159 Hill, R S., 133, 134, 135, 136, 137, 138, 139, 142, 153 Hillis, D M., 4, 119, 120, 155 Historical associations, 101, 102, 103, 105 Historical biogeography approaches: definitions, 11–13; main characteristics, 14–16 Historical biogeography techniques, 17 Holmes, E C., 156 Homogenization See Biotic homogenization Honeycutt, R L., 127 Hooker, J D., 31, 134 Horizontal transference See Historical associations Host See Event-based methods Host-switching, 102 Host tracking, 102 Hot spots, 166 Hovenkamp, P., 17, 24 Huelsenbeck, J P., 17, 111, 112, 156, 192, 200 Humphries, C J., 5, 11, 17, 25, 33, 38, 39, 57, 67, 68, 83, 91, 133, 134, 138, 142, 143, 162 Hunn, C A., 153 Hypotheses in historical biogeography, 146–148 Individual tracks: definition, 11, 54, 55; orientation, 56 Integrative method, 17; definition, 81 Interspecific coalescence, 102 Invasions See Species introduction Invertebrates, by taxonomic genus: Aeghorhinus, 115; Antarctobius, 115; Apodrassodes, 97; Bassaris, 9; Boeckella, 62; Drosophila, 126; Echemoides, 97, 114; Eriococcus, 83; Falklandius, 115; Germainiellus, 115; Grella, 126; Ixodes, 126; Index Listroderes, 96; Madarococcus, 83; Melanoplus, 126; Mendizabalia, 96; Nannochoristina, 83; Oxelytrum, 83; Pimelia, 159; Ptomaphila, 83; Puranius, 115; Rhyephenes, 115; Vanessa, Island biogeography, 162, 177 Islands: and molecular biogeography, 159; and biotic exchange, 174–175; and species introduction, 176, 178 Isthmus of Panama, 34, 158 Japan, 126 Jordan, G J., 134 Juan, C., 159 Jungles, 17; definition, 111 Katinas, L., 3, 49, 61, 138, 145, 168, 185 Keast, A., 54 Kitching, I J., 3, 186 Kluge, A G., 77, 188 Knox, E B., 41, 153 Krzywinski, J., 153, 159 Kuhn, T S., 5, 180 Ladiges, P Y., 9, 17, 68, 69, 77, 79, 85, 134, 138, 142, 143, 144, 196 Lakatos, I., 33 Lamarck, J.-B., 185 Larget, B., 192, 201 Lauraceae, 159 Lavin, M., 117, 152, 153 Lewis, P O., 191 Lieberman, B S., 7, 8, 9, 11, 72, 75, 77 Liebherr, J K., 85 Liliales, 117 Limacoidea, 52 Linder, H P., 27, 85, 99, 108, 117, 134, 136, 138, 143, 144 Lineage sorting, 102 Linnaeus, C., 30 Lobeliaceae, 41 Lomolino, M B., 161, 175, 178 Lopretto, E C., 99 Luna, I., 99 Lundberg, J G., 88 Lundberg rooting, 88, 89 Lydeard, C., 81 Lyell, C., 31 Macaronesia, 159 MacArthur, R H., 177 MacRae, A F., 157 Maddison, D., 202 Maddison, W., 202 Madeira Islands, 157–158 Magellanic Forest, 114–116, 171, 172 Magellanic Moorland, 114–116, 171, 172 Main massing, 56, 57 Malhotra, A., 157 Mallet, J., 167 Malpighiaceae, 159 Malvinas Islands, 114–116 Mann, D M., 99 Manos, P S., 134, 138, 139, 140 Marino, P I., 99 Markov chain Monte Carlo algorithm, 156, 192 Márquez, J., 92 Marshall, C J., 85 Marshall, L G., 36 Martin, P G., 134, 136 Maternal inheritance, 118, 120 Matthew, W D., 11, 17, 31 Mau, B., 192 Maule, 114–116 Maximum cospeciation See Reconciled trees Maximum likelihood See Phylogenetic reconstruction Maximum parsimony algorithms: and areas of endemism, 26; in cladistic biogeography, 72, 74, 75, 77, 79, 81, 115; in parsimony analysis of endemicity, 87, 89, 90; in cladistic methods, 188, 189; software, 198–200 Mayden, R L., 57 Mayr, E., 31 McAllister, D E., 54 McLaughlin, S P., 86 McLennan, D A., 75, 85 245 246 Index Meacham, C., 59 Mean propinquity method, 22 Melastomataceae, 159 Melville, R., 136 Metallicina, 83 Metricity, 113–114 Mickevich, M F., 17 Miller, R L., 164 Miocene, 35, 66 Miranda-Esquivel, D R., 26, 90, 91, 112, 117 Mitochondrial DNA See DNA Models, 2, 5, 9, 13, 14, 15, 16; in event-based methods, 12–13, 100, 108, 110, 112; in experimental biogeography, 127, 128, 129, 130, 131 Molecular biogeography, 152; and islands, 159 Molecular clock: and dispersalism, 33; application in biogeography, 125–126; definition and biogeographic utility, 153– 157; calibration, 155–156; tests, 156; applied to Anthus, 157–158 Molecular phylogenies: and sampling, 29; of Nothofagus, 134; in biogeography, 151– 152; Anthus, 157–158; research using, 159; data, 188–189, 190 Molecular systematics, 3, 4; and eventbased methods, 100; applied to phylogeography, 125; related to biogeography, 151–159 Monjeau, J A., 22 Mooers, A Ø., 164 Mooi, R D., 25, 26, 28 Moore, D M., 136, 169 Moore, P D., 2, Morell, P L., 159 Moritz, C., 167, 168 Morrone, J J., 3, 4, 17, 22, 24, 25, 26, 27, 50, 54, 60, 61, 66, 68, 81, 82, 85, 87, 90, 92, 96, 99, 109, 112, 114, 127, 148, 167, 181, 182 Müller, F., 185 Müller, P., 26 Multiple lineage, 102 Multiplication of lineages, Multistate characters: in PAE, 89; in ancestral areas method, 45 Muss, A., 126 Myers, A A., 2, 92 NCA See Nested clade analysis Nee, S., 151 Nelson, G., 3, 4, 7, 9, 12, 17, 23, 25, 28, 33, 57, 67, 68, 69, 77, 79, 82, 134, 138, 142, 196 Nested areas, 167, 173 Nested clade analysis, 123–124 Nested clade distance, 124 New Caledonia, 132–134, 138–146 New Guinea, 132–134, 138–146 Newton, M., 192 New Zealand, 41, 61–62, 66, 82–85, 132–134, 138–146, 178 Nielsen, R., 156 Nixon, K., 201 Node, in panbiogeography, 12, 57, 167 Nordlander, G., 117 North America, 34–36, 85, 17, 121, 126, 157– 158 North Atlantic region, 126 Northern Hemisphere, 159 Nothofagus See Southern beeches Nylin, S., 17, 77, 108 Oligocene, 50, 66 Oliver, W R B., 135 Olmstead, R G., 159 One area per species assumption, 106 Optimality criteria: for areas of endemism, 28; for event-based methods, 100 Ortiz Jaureguizar, E., 181 Ortologous genes, 102 Outgroup method, 186 PAE See Parsimony analysis of endemicity Page, R D M., 17, 54, 68, 69, 72, 77, 79, 81, 100, 101, 104, 111, 112, 114, 139, 156, 196, 197, 201 Paleozoic, 63 Index Palmer, J D., 41, 153, 159 Palmer, M., 85 Panamanian land bridge See Isthmus of Panama Panbiogeography, 14, 17; definition, 11; individual tracks, 11, 54, 55, 56; generalized tracks, 11, 57; main characteristics, 15–16; node, 57; criticisms 57–58; track compatibility, 58–60; case studies, 61–66; research using, 66; using Nothofagus, 145–146; and biodiversity conservation, 162, 166–167, 168–169; software, 195 Paralogous genes, 102 Paralogy, in historical associations, 102 See also Geographic paralogy Paralogy-free subtrees, 17; definition, 78–81, 80; case study, 97; and molecular data, 153 Páramo, 61, 62, 63, 95 Parasite See Event-based methods Parasite extinction, 102 Parenti, L R., 5, 25, 33, 38, 39, 67, 68, 138, 143 Parsimony algorithms See Maximum parsimony algorithms Parsimony analysis of endemicity, 14, 17; definition, 12, 86–87; main characteristics, 15–16; phylogenetic information addition, 88–89; based on localities, 88–90; based on areas of endemism, 88–90; based on quadrats, 90–92, 91; case studies, 92–99; research using, 99; and biodiversity conservation, 91, 162, 167, 169–173; criticisms, 91–92 Pascual, R., 36, 181 Patagonia, 61, 62, 63, 64, 65, 95 Pattern-based methods, Patterson, A M., 101 Patterson, C., 57, 83 Patton, L., 124, 126 Pauling, L., 154 Perú, 49 Pests, 126 Philipson, N N., 134 Philipson, W R., 134 Phylogenetic biogeography, 14, 17; definition, 11, 37; main characteristics, 15– 16; progression rule, 37–38; deviation rule, 38; methodology, 38; criticisms, 39; case study, 39–41; and molecular data, 153 Phylogenetic indexes See Phylogenetic measures for conservation Phylogenetic measures for conservation, 164 Phylogenetic reconstruction: cladistic methods, 185–190; maximum likelihood methods, 191–192; bayesian methods, 192; distance methods, 192–193 Phylogeny, 3, 14, 15, 185–193; and panbiogeography, 56 Phylogeography, 14, 17; definition, 13, 118– 119; main characteristics, 15–16; hypotheses, 121; corollaries, 123; nested clade analysis, 123; case study, 124–126; research using, 126; and biodiversity conservation, 162, 167–168; software, 198 Plants, by taxonomic genus: Abrotanella, 52; Aesculus, 159; Argyranthemum, 159; Aristotelia, 61–62, 83, 144; Bencomia, 159; Bromheadia, 52; Calopappus-Nassauvia, 96; Caryota, 159; Chuquiraga, 52; Cornus, 159; Crinodendron, 83; Depanthus, 83; Drapetes, 83; Drimys, 83; Dubouzetia, 83; Fagus, 83, 126; Gilia, 159; Helleborus, 159; Leucheria, 96; Moscharia, 49–51, 55; Negria, 83; Nothofagus, 6, 57, 83, 132–148; Oreomyrrhis, 83; Peripentadenia, 83; Phippsia, 126; Pictetia, 117; Polyachyrus, 49–51; Rytidosperma, 117; Smilax, 29; Solanum, 159; Styrax, 52, 117, 159; Triptilion, 96 Platnick, N I., 3, 7, 12, 17, 23, 25, 28, 33, 57, 67, 68, 69, 77, 82, 161, 162 Pleistocene, 2, 34–35, 66, 126, 158 Pliocene, 34, 35, 35, 158 Podonominae, 41 Pole, M., 136 Polhemus, D A., 82 Popper, K R., 182 247 248 Index Posada, D., 124, 198 Posadas, P., 17, 26, 66, 90, 91, 92, 99, 109, 112, 114, 138, 140, 164, 167, 169 Prance, G., 162 Predicted dispersal See Dispersal Progression rule, 38 See also Phylogenetic biogeography Pseudopsinae, 83 Psiphlonuridae, 83 Puna, 61, 62, 63, 95 Quantification of component analysis, 17 Quantitative phylogenetic biogeography, 17 Quaternary, 50 Rahel, F J., 178 Random dispersal See Dispersal Rannala, B., 192 Rapoport, E H., 22 Ratites, 57, 146 Raven, P H., 31, 135, 136 Reconciled trees, 17; definition, 101–108, 107; case study, 114–116; applied to Nothofagus, 139–140, 144–145; and molecular data, 153 Reduced area cladogram, 17 Redundancy, 9, 102 Redundant distribution, 49, 68–71 Renner, S S., 159 Repetur, C P., 52 Rich, S M., 126 Riddle, B R., 127 Ringuelet, R A., 64 RNA, 151 Robichaux, R H., 159 Roig-Juñent, S., 26, 27 Romesburg, H C., 147 Ron, S R., 99 Ronquist, F., 7, 8, 9, 17, 45, 46, 47, 77, 106, 108, 109, 110, 114, 115, 119, 138, 140, 157, 197, 200 Roos, M C., 17, 69, 196 Rosen, B R., 12, 17, 24, 86, 87, 88, 89 Rosen, D E., 12, 17, 67, 182 Ross, H H., 37 Rozas, A., 126 Ryder, O A., 167 Sala, O E., 6, 160, 174, 175, 176 Salisbury, B A., 60, 64, 195 Sanderson, M J., 155 Sanmartín, I., 117 Sawyer, J W D., 181 Schuh, R T., Schuster, R M., 135 Seberg, O., 57, 134, 138 Sempere, T., 36 Sequeira, A S., 156 Setoguchi, H., 134 Sharp, P M., 156 Simon, D L., 192, 201 Simpson, B B., 66 Simpson, G G., 31, 34, 35, 154 Simpson Vuilleumier, B B., 66 Simuliini, 117 Simultaneous speciation, 102 Smith, A B., 86, 88, 92 Software See Computer programs Sorting events See Historical associations Soulé, M E., 178 South Africa, 82–85 South America, 34–36, 41, 49–52, 61–66, 82– 85, 99, 114–116, 132–134, 138–146, 157– 158, 159, 168–169 South American mountain ranges, 63–66 Southeast Asia, 52, 159 Southern beeches (Nothofagus): extant species distribution, 133; biogeographical hypotheses, 134–136; research using, 138– 146 Southern Hemisphere, 52, 66, 85, 132, 146 Southern South America, 49–52, 82–85, 99, 114–116, 132–134, 138–146, 168–169 South Georgia Islands, 157–158 Spanning graphs, 17 Spanning tree, 59 Spatial analysis: definition, 5; spatial pre- Index diction, 5; space-time processes, 5, 6–9; spatial postdiction, 5, 9; spatial arrangement, 5–6 Spatial homology: definition, 9; recognition, 81; and conservation, 166 Species introduction: biotic exchanges, 174– 175; and biogeography, 175; biological invasions, 176–177; invasion consequences, 178–179 Species richness, 162 Spellerberg, I F., 181 Steel, M A., 191 Stheli, F G., 36 Stochastic biogeography See Experimental biogeography Stuessy, T F., 66, 186 Subantarctic, 61, 62, 63, 95, 114–116 Successive specialization, 102 Sun, H., 159 Swenson, U., 52, 135, 136, 137, 138, 139, 140, 142, 153 Swofford, D L., 3, 72, 191, 192, 193, 199 Sympatry, 9, 102 Sytsma, K J., 159 Takezaki, N., 157 Takhtajan, A., 27 TAS See Three-area statements Tasmania, 41, 132–134, 138–146 Taxon biogeography, 9, 138–142, 148 Taxonomic distinctness, 164 Taxonomy of methods, 10 Templeton, A R., 123, 124, 181, 198 Tertiary, 34 Thorpe, R S., 157 Three-area statements, 17; criticisms, 77; definition, 77, 78; case study, 96–99 Three-dimensional cost matrix, 106, 110– 111, 113 Tierra del Fuego, 169–173 Timing in historical biogeography, 153–157 Track analysis, 17 Track compatibility, 17; definition, 58–60; case study, 63–66 Trans-Pacific areas, 66 Trejo-Torres, J C., 99 Tuffley, C., 191 Turtles, 126 Two-dimensional cost matrix, 108 Udvardy, M D F., 22 Ulfstrand, S., 162 Upchurch, P., 153 Urtubey, E., 85 Vagility, 130 Valdivia, 114–116 Vander Zanden, M J., 175 Vane-Wright, R I., 164 Van Steenis, C G G J., 132, 136 van Veller, M G P., 11, 68, 69, 72, 75, 77 Vertebrates, by taxonomic genus: Anthus, 52, 117, 157–158; Dactylomis, 125; Dasypus, 35; Didelphis, 35; Echymis, 125; Eremotherium, 35; Euproctus, 159; Felis, 35; Geomys, 120; Isothrix, 125; Leiopelma, 57; Makalata, 125; Mesomys, 125; Neotoma, 126; Ophioblennius, 126; Tapirus, 35; Tayassu, 35 Vicariance, 6, 7, 8, 9, 13, 15, 102, 104, 105, 109–110, 129–130 Vicariance events technique, 17 Vicariant biogeography See Experimental biogeography Vinnersten, A., 117 Vitousek, P., 174, 178 Voelker, G., 52, 117, 155, 157 Walker, D E., 126, 167 Wallace, A R., 30, 135 Waters, J M., 34, 156, 159 Webb, S D., 36 Weddellian province, 138–139 Wegener, A., Weston, P H., 33, 134, 142 Widespread taxa, 68–71 Wiley, E O., 17, 31, 38, 69, 72 Williams, W T., 114 249 250 Index Willink, A., 27, 50, 95, 96, 114 Wilson, E O., 177 Wilson, R J., 54 WISARD, 17 Wolfe, K H., 156 Xiang, Q Y., 159 Yang, Z., 192 Zandee, M., 17, 69, 196 Zink, R M., 117, 119 Zuckerkandl, E., 154 Zullini, A., 22 Zunino, M., 22 ... rearrangement of continental land masses and islands and the opening and closing of sea and ocean basins initiated by these movements and interactions have profoundly affected the distribution and... and dispersal, phylogenetic biogeography, cladistic biogeography, and eventbased methods The other four, ancestral areas, panbiogeography, parsimony analysis of endemicity, and experimental biogeography, ... dispersal explanation as the main process in biogeography and promote vicariance as an equally important process Currently both vicariance and dispersal are recognized as significant biogeographic