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In these essays that survey the burgeoning field of tropical herpetology, former students and associates pay tribute to Jay Savage's four decades of mentoring. The result is a book unlike any other available in tropical herpetology. Covering a wide array of subjects, Ecology and Evolution in the Tropics is the first book in more than two decades to broadly review research on tropical amphibians and reptiles. A tribute to Savage and an invaluable addition to the herpetological literature, this work will be cited for years to come.

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Ecology & Evolution in the Tropics

The University of Chicago Press

Contents

Foreword by Luis D. Gmez........................................................................................................................................................................xiPreface..........................................................................................................................................................................................xiiiPart I: Evolution and Biogeography1. Taxonomy in Theory and Practice, with Arguments for a New Phylogenetic System of Taxonomy Arnold G. Kluge....................................................................................72. Biogeography and Molecular Phylogeny of Certain New World Caecilians Marvalee H. Wake, Gabriela Parra-Olea, and Judy P.-Y. Sheen.............................................................483. Diversity of Costa Rican Salamanders David B. Wake...........................................................................................................................................654. On the Enigmatic Distribution of the Honduran Endemic Leptodactylus silvanimbus (Amphibia: Anura: Leptodactylidae) W. Ronald Heyer, Rafael O. de S, and Sarah Muller.........................815. Chromosomal Variation in the rhodopis Group of the Southern Central American Eleutherodactyline Frogs (Leptodactylidae: Eleutherodactylus) Shyh-Hwang Chen...................................1026. The Physiological Basis of Sexual Dimorphism: Theoretical Implications for Evolutionary Patterns of Secondary Sexual Characteristics in Tropical Frogs Sharon B. Emerson.....................1457. Higher-Level Snake Phylogeny as Inferred from 28S Ribosomal DNA and Morphology Mary E. White, Maria Kelly-Smith, and Brian I. Crother.........................................................1568. Elapid Relationships Joseph B. Slowinski and Robin Lawson....................................................................................................................................1749. Wallace and Savage: Heroes, Theories, and Venomous Snake Mimicry Harry W. Greene and Roy W. McDiarmid.........................................................................................190Part II: Ecology, Biogeography, and Faunal Studies10. Quantification of Selection and Male Reproductive Success in Hyla calypsa, a Neotropical Treefrog Karen R. Lips.............................................................................21511. Patterns of Co-occurrence of Hylid Frogs at a Temporary Wetland in Costa Rica Craig Guyer and Maureen A. Donnelly...........................................................................22712. It's a Frog-Eat-Frog World in the Paraguayan Chaco: Food Habits, Anatomy, and Behavior of the Frog-Eating Anurans Norman J. Scott Jr. and A. Luz Aquino......................................24313. Long-Term Frog Monitoring by Local People in Papua New Guinea and the 1997-98 El Nio Southern Oscillation David P. Bickford................................................................26014. Historical Biogeographic Relationships within the Tropical Lizard Genus Norops Kirsten E. Nicholson.........................................................................................28415. Hypotheses on the Historical Biogeography of Bothropoid Pitvipers and Related Genera of the Neotropics Steven D. Werman......................................................................30616. The Herpetofauna of the Rincn Area, Pennsula de Osa, Costa Rica, a Central American Lowland Evergreen Forest Site Roy W. McDiarmid and Jay M. Savage.......................................36617. The Iwokrama Herpetofauna: An Exploration of Diversity in a Guyanan Rainforest Maureen A. Donnelly, Megan H. Chen, and Graham G. Watkins.....................................................42818. The Herpetofauna of the Guayana Highlands: Amphibians and Reptiles of the Lost World Roy W. McDiarmid and Maureen A. Donnelly................................................................461References.......................................................................................................................................................................................561Contributors.....................................................................................................................................................................................627Subject Index....................................................................................................................................................................................631Taxonomic Index..................................................................................................................................................................................655

Chapter One

Arnold G. Kluge

Theory without fact is fantasy, but facts without theory is chaos. CHARLES OTIS WHITMAN

Taxonomy as it is currently practiced is nearly 250 years old, and it is only now undergoing its first major revolution (Pennisi 1996). There is widespread agreement that categorical ranks must go, and with this change alone there is repudiation of what has been to date the venerable Linnaean approach to classification (Linnaeus 1758; see review in Ereshefsky 2001) as well as the rejection of the well-entrenched International Codes of Nomenclature (ICBN 1994; ICNB 1992; ICZN 1999). Making explicit connections to evolutionary theory and phylogenetic hypotheses is also considered important to the modernization of taxonomy. The issues underlying these attacks on the Linnaean tradition are especially complex because they involve the whole of science, from the philosophical to the pragmatic (Ereshefsky 2001). My attempt to understand the theory and practice of taxonomy, including the current revolution, is founded largely on the distinction between classification and systematization (Griffiths 1974; see also Griffiths 1973, 1976). Most of the discussion to follow explores the role science plays in systematization, and with that understanding I propose and exemplify a new phylogenetic system of taxonomy.

Definitions and Distinctions

There are several different kinds of definitions, which unfortunately are conflated in ordinary discourse, and whose record of use in science is not much better. Particularly important terms in distinguishing the classification of Linnaeus from the systematization of G. C. D. Griffiths are extension, intension, and ostension (table 1.1). Intension is used to define universals. Ostension and extension are used to define particulars. Extensional definitions, however, may look like intensional definitions, thus opening the door for confusion such that particulars seem to be defined in universal terms. Also potentially confusing are those things that may be judged abstract (table 1.1), such as the Equator and the North and South Poles. Suffice it to say that these kinds of particulars are not so abstract as to keep us from knowing when we have crossed the Equator or have arrived at either of the Poles.

Intension (connotation) is the principle according to which a class, or set, of things is picked out; it is the condition a thing must satisfy to be precisely described by the predicate (Blackburn 1994). Intension involves a defining rule whereby members are included, or excluded, from the set. The conditions are the properties common to all those things (and only them) that are referred to by a word (Angeles 1992). Definition from intension is a form of prescription, because the members of a set are prescribed as necessarily having certain qualities. Prediction requires intensional definition, and that kind of definition is important in the identification of properties that may constitute a generality, such as a universal law of nature (Kluge 2003b).

Ostension is definition by reference, by enumeration or pointing at particulars (by showing the object to which a name is given). This kind of definition is used in identifying configurational and contingent relations, as in the case of a particular taxon and its historical relationships.

Definition from extension is a form of ostension, and it is also used to define particulars. Extensional definitions appear to differ from intensional ones only semantically, but this is not really the case. Consider that the denotation of a predicate is the class of things (extensions) that a term (intension) picks out. For example, the extension of the universal "red" is the class of red things (particulars) (Blackburn 1994). Extension can also be used to evaluate the characteristics of the members of a demarcated class, in order to formulate a defining "rule" (a descriptive generalization) written in the form of an intension.

Classification is the orderly arrangement of a set of particulars that instantiate some intensionally defined, abstract, generality-a universal, or what some would call a natural kind (tables 1.1, 1.2). For example, the Periodic Table is a classification, one of material essentialism, in which an element's place in the table is defined intensionally according to the inherent property of atomic number-the number of protons possessed by the element. Thus, gold and lead are classified (ordered) in relation to each other, and to other elements in the table, according to their atomic numbers, 79 and 82, respectively. To obtain gold from lead does nothing to the intensionally defined categories of either "goldness" or "leadness." There still exists a place in the Periodic Table for atomic numbers 79 and 82. Atomic theory is the major premise underlying the Periodic Table, with the table successfully predicting elements new to science. Because predictiveness is considered a condition of natural laws, atomic theory is spoken of in law-like terms (table 1.1).

Laws of nature, and their accompanying theories, are subject to critical testing and revision, and even rejection. For example, in formulating the original version of the Periodic Table in 1871, Mendeleyev defined the classification in terms of atomic weight. At that time, gold and lead were intensionally defined as having weights 197.2 and 207.2. In 1942, the definition of lead was changed to 207.21. In spite of these kinds of redeterminations of atomic weights, some of the elements in Mendeleyev's Periodic Table were still required by their properties to be put in positions out of order of atomic weight. The problem was resolved when the structure of the atom became better understood, whereupon the Periodic Table was defined according to the theory of atomic number. Webb et al.'s (2001) recent findings that call into question the constancy of the speed of light further illustrate that no scientific theory is immune to testing, even one of nature's most well-known laws.

All of the historical entities in the new phylogenetic taxonomy proposed herein, those that I call phylospecies, and the more inclusive parts of history to which they belong, can be systematized, because they are naturally related to one another (see the following section). Particular instances of those kinds of historical entities are not matters of intensional definition, because they are not prescribed in terms of inherent qualities, that is, properties necessary and sufficient for membership in some group. This is unlike such abstractions as the categorical ranks of the traditional Linnaean and annotated classifications, which can only be instantiated by qualitatively defined things, things analogous to the instances of the elements in the Periodic Table. In no sense can there be laws of history (Popper 1957). History is not predictable (e.g., contra Schwenk 1994; Griffiths 1999), even though the retrodiction of trends in phylogenetic history is undeniable. History simply is, and its retrodiction is potential only in the marks it may leave that are not subject to an information-destroying process (Sober 1988, 3-5).

The parts of phylogenetic history, such as species and the more inclusive groups to which they belong, must be testable and subject to revision for the system to be considered scientific (Kluge 1999, 2003a). This involves the use of discovery operations that are capable of exposing false hypotheses and providing novel, testable explanations. Those operations must be ideographic (historical, retrodictive), given the nature of the system. They cannot be nomothetic (universal, predictive) (Grant 2002).

From the Philosophical to the Pragmatic

INDIVIDUATING HISTORICAL ENTITIES

The importance of individuation in taxonomy is clear. As Quine (1958, 1960) convincingly argued, there can be "no entity without identity" if language is to express proper scientific facts. The individuation of historical entities is straightforward because they are naturally related to one to another by virtue of inheritance (Darwin 1859, chap. 13; Ghiselin 1966; Hull 1978). Indeed, those entities are self-defining because of the causal relation of inheritance, and it is that self-definition that provides the basis for their objectivity. It is then the causal relation of inheritance that constitutes the basis for the system of taxonomy (table 1.1). The system is genealogical, that which represents the natural, hierarchical arrangement of species.

A PHYLOGENETIC SPECIES CONCEPT

A rigorous scientific research program requires that an abstract, theoretical definition of a class of particulars (table 1.1) logically precede the formulation and testing of the discovery operations designed to detect those things (Grant 2002). For example, Kluge (1990, 423) defined the concept species as "the smallest historical individual within which there is a parental pattern of ancestry and descent." This definition follows from Darwin's (1859) theory of evolution, "descent, with modification," from those conditions pertaining to the inheritance of historical individuals, and from the prevailing notion that species are the effects of evolution, not effectors (Lidn 1990). Note that this definition of species does not presuppose any discovery operation, nor that the entities are of any particular kind, bisexual or asexual, and extant or extinct.

Kluge (1990, 422; see also Hull 1980; Sober 1991; de Queiroz et al. 1995) also drew attention to the distinction between historical and contemporary individuals (table 1.1). Contemporary individuals, such as a population or a deme, are less inclusive than historical individuals, and although all kinds of contemporary individuals are historical, insofar as they are extended in time, their unity is the result of the cohesive and integrative processes of their replicator-continuum (Lidn 1990). In contrast, historical individuals are united by common history, not by their current interactions.

The most inclusive entity in a historical system is earth-bound life, whereas the least inclusive entity is the smallest historical individual, the phylogenetic species, or more simply what I call phylospecies. Although the concept of phylospecies, as defined above, does not necessarily exclude any scientific discovery operation, the identification of phylospecies, as well as the natural groups of which they are a part, will quite likely involve phylogenetic systematic analysis (Hennig 1966). In that regard, the identification of phylospecies is consistent with the scientific goals of the phylogenetic system of taxonomy proposed in this chapter. The phylospecies concept is then not the same as the operational phylogenetic species concept that requires fixed character differences (e.g., sensu Eldredge and Cracraft 1980; Cracraft 1983; see also Vrana and Wheeler 1992; for review, see Frost and Kluge 1994).

Asexual phylospecies can be discovered just like bisexuals, according to phylogenetic systematic analysis (Kluge 1990). Asexuals may as well be judged good phylospecies in theory (Kluge 1990). They are historically connected and exhibit inherited traits, just as bisexuals do. Although asexuals do not engage, at least regularly, in those processes that lead to the cohesiveness of bisexual populations, such as gene flow and genetic homeostasis, nonetheless they may be rendered "cohesive" by developmental canalization as well as by natural selection acting on the similar behavioral and ecological traits that they have inherited. Thus, the phylospecies concept is unique in that it covers the extant as well as the extinct, and bisexuals as well as asexuals (Ereshefsky 2001).

Having explicated phylospecies, we can consider certain fundamentals relating to their origin. Arguing by analogy, we cannot liken the origin of phylospecies to reproduction, gestation, and birth. These are the kinds of processes that are identified with the origin of contemporary individuals and can only apply metaphorically to the singular model of species (Lidn 1990, 184). Rather, the origin of phylospecies is like mitosis or schizogony (replication by fission) (Frost and Kluge 1994). If we assume the latter analogy, the process of phylospecies origination should be termed phylogenesis (Hennig 1965, 97). Phylogenesis is then the patterns and processes relating to the origin of the smallest historical individuals (e.g., see Cracraft 1992; Hovenkamp 1997), as distinct from speciation, which involves the replicator-continua of populations and genes. Arguably, phylogenesis in asexuals is also one of fission. Lidn (1990, 184) makes especially clear the nature of those studies that focus on historical individuals: "Macroevolution ... can be defined as differential [phylogenesis] and extinction (sorting) of gene pool continua, which in turn of course leads to change in diversity at higher (taxa) levels, but as integrating processes are lacking, a 'hierarchical theory of evolution' ... above the level of replicators is theoretically empty.... If the clades manifested as Aves and Anemone nemorosa become extinct, they do so as a sum of replicators. We do not need theories for that!"

I do not object to using the terms species and speciation, providing they are nominal, or taken to mean phylospecies and phylogenesis, respectively. Phylospecies should not be equated to the Linnaean categorical rank of species, or to any one of the familiar qualitative conceptualizations of species, such as those definitions having to do with interbreeding (Mayr 1970, 12; Paterson 1985) or ecological (Van Valen 1976) processes. An exclusive use of phylospecies and phylogenesis, rather than species and speciation, clearly sets systematization apart from classification and the population/process thinking of the neo-Darwinian synthesis, the latter not being concerned with historical individuality but with the replicator-continua of populations and genes. As Lidn (1990; see also Gardiner 1952) has emphasized, the study of contemporary individuals is legitimate in its own right, but it must not be confused with necessarily unique particulars, like phylospecies, and the study of their origin and extinction.

MONOPHYLY

In a taxonomic system defined in terms of inheritance, each taxon is a historical individual; it is a spatiotemporally restricted, as well as necessarily unique, part of phylogeny (Kluge 1990, 1997, 1998a, 1999; Siddall and Kluge 1997). Therefore, each historical individual is monophyletic; "A 'thing' cannot be paraphyletic" (Lidn 1990, 183; contra de Queiroz and Donoghue 1988). The monophyly of taxa inclusive of two or more phylospecies follows Hennig's (1966) definition, that is, an ancestor and all of the phylospecies hypothesized to have evolved there from. The ancestor, or common ancestral phylospecies, "is identical with all of the species that have arisen from it" (Hennig 1966, 71; my emphasis); it is not one of the parts of the more inclusive taxon being defined ostensively. Neither does a common ancestral phylospecies depend on an operationalism for its existence. It is irrelevant, for example, that few, if any, of the common ancestral species that have been hypothesized have survived all of the empirical tests demanded by phylogenetic systematic analysis. Moreover, that common ancestral species are verified all the time with so-called missing links is irrelevant, because those induced speculations involve special knowledge, such as plausible adaptive scenarios, or overall similarity. These are not scientific tests, because there is no attempt to disconfirm competing hypotheses of relative recency of common ancestry (Kluge 2003b).

In the case of phylospecies, monophyly concerns only a spatiotemporally restricted, necessarily unique point of origin. In the parlance of phylogenetic systematics, the monophyly of phylospecies does not include sister or common ancestral lineages. This interpretation of monophyly is substantially different from that of evolutionary systematists, who define monophyly in terms of process, for example, as the "natural outcome of the evolutionary process" of descent (Donoghue and Cantino 1988, 107), the occurrence of "long-term extrinsic [zoogeographic] barriers to gene flow" (Avise et al. 1987, 517), or "the stage ... at which point neither species is 'paraphyletic' with respect to the other" (Goldstein and DeSalle 2000, 371). As an example of what is wrong with process as a definition, paraphyletic species can become monophyletic if the excluded part were to go extinct. Consider further that in the case of the biological species concept, all paraphyletic sets of interbreeding populations have the potential to become monophyletic.

(Continues...)

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