_This sweeping discussion of the philosophy of evolutionary biology is based on the revolutionary idea that species are not kinds of organisms but wholes composed of organisms._.

The long-awaited revision of the industry standard on phylogenetics Since the publication of the first edition of this landmark volume more than twenty-five years ago, phylogenetic systematics has taken its place as the dominant paradigm of systematic biology. It has profoundly influenced the way scientists study evolution, and has seen many theoretical and technical advances as the field has continued to grow. It goes almost without saying that the next twenty-five years of phylogenetic research will prove as fascinating as the (...) first, with many exciting developments yet to come. This new edition of Phylogenetics captures the very essence of this rapidly evolving discipline. Written for the practicing systematist and phylogeneticist, it addresses both the philosophical and technical issues of the field, as well as surveys general practices in taxonomy. Major sections of the book deal with the nature of species and higher taxa, homology and characters, trees and tree graphs, and biogeography—the purpose being to develop biologically relevant species, character, tree, and biogeographic concepts that can be applied fruitfully to phylogenetics. The book then turns its focus to phylogenetic trees, including an in-depth guide to tree-building algorithms. Additional coverage includes: Parsimony and parsimony analysis Parametric phylogenetics including maximum likelihood and Bayesian approaches Phylogenetic classification Critiques of evolutionary taxonomy, phenetics, and transformed cladistics Specimen selection, field collecting, and curating Systematic publication and the rules of nomenclature Providing a thorough synthesis of the field, this important update to Phylogenetics is essential for students and researchers in the areas of evolutionary biology, molecular evolution, genetics and evolutionary genetics, paleontology, physical anthropology, and zoology. (shrink)

Geographic coincidence of animal and plant distributions to form recognizable patterns suggests that the separate components of the patterns are historically connected with each other and with geographic history. To seek evidence of these historical connections, cladograms of geographic areas, representing sequences of disruptive geologic, climatic, or geographic events, may be compared with biological cladograms, representing sequences of allopatric speciation events in relation to those geographic areas. Such comparisons, when they meet the minimum requirements of being among dichotomized threetaxon cladograms, (...) can resolve similar or dissimilar historical factors; two-taxon statements do not distinguish between groups with different histories. Congruence of biological and geological area-cladograms at a high confidence level (such as congruence of a five-taxon cladogram or four three-taxon cladograms with a geological cladogram, where the confidence level can be shown in cladistic theory to be 99%) means that specified events of paleogeography can be adopted as an explanation of the biological patterns. In such a cause and effect relationship, where the earth and its life are assumed to have evolved together, paleogeography is taken by logical necessity to be the independent variable and biological history, the dependent variable. Drawing a mathematical simile, the biological cladogram y (dependent variable), is a function of the geological cladogram x (independent variable), as in a simple regression of effect y on cause x where we are given no free choice as to which is the independent variable. Such a view implies that any specified sequence in earth history must coincide with some discoverable biological patterns; it does not imply a necessary converse that each biological pattern must coincide with some discoverable paleogeographic pattern, because some biological distributions might have resulted from stochastic processes (chance dispersal). Determining that all discoverable biological patterns conflict with a given corroborated or observed sequence of geologic, climatic, or geographic change (i.e., that y is not a function of x), in theory, therefore should falsify vicariance biogeography. Because dispersal biogeography presupposes stochastic processes, and any failure to meet the expectation of a postulated dispersal is explained by an additional dispersal, dispersal biogeography is immune to falsification. Without resort to paleontology or earth history, whether a given historical relationship implied by congruence of biological area-cladograms is the result of dispersal or vicariance can also be thought of in terms which minimize the number of necessary assumptions: did the sedentary organisms disperse with the vagile ones or did the vagile organisms vicariate with the sedentary ones? Cladistic congruence of a group of sedentary organisms with a group of vagile ones rejects dispersal for both. Hence, distributions of sedentary organisms have the potential to falsify dispersal theories as applied to vagile organisms, but distributions of vagile organisms cannot falsify vicariance theories as applied to sedentary ones. The problems that arise in various kinds of historical explanation are exemplified by several specific distributions of fishes and other organisms in North and Middle America and in the larger context of Pangaean history, and are discussed in relation to current species concepts. (shrink)

At least 22 concepts of species are in use today and many of these are notably incompatible in their accounts of biological diversity. Much of the traditional turmoil embodied in the species problem ultimately derives from the packaging of inappropriate criteria for species into a single concept. This results from a traditional conflation of function of concepts with their applications, definitions with concepts, taxonomic categories with groups, and the ontological status of real species with teleological approaches to recover them. Analogous (...) to classifications of supraspecific taxa, our forging inappropriate and ambiguous information relating to theoretical and operational discussions of species ultimately results in a trade-off between convenience, accuracy, precision, and the successful recovery of natural biological diversity. Hence, none of these expectations or intentions of species or classifications is attainable through composite, and possibly discordant, concepts of biological diversity or its descent. Reviewing and evaluating the concepts of species for their theoretical and operational qualities illustrates that a monistic, primary concept of species, applicable to the various entities believed to be species, is essential. This evaluation reveals only one theoretical concept as appropriate for species, the Evolutionary Species Concept. This conceptualization functions as a primary concept and is essential in structuring our ideas and perceptions of real species in the natural world. The remaining concepts are secondary, forming a hierarchy of definitional guidelines subordinate to the primary concept, and are essential to the study of species in practice. Secondary concepts should be used as operational tools, where appropriate, across the variance in natural diversity to discover entities in accord with the primary concept. Without this theoretical and empirical structuring of concepts of species our mission to achieve reconciliation and understanding of pattern and process of the natural world will fail. (shrink)

Argues for the primacy of the phylogenetic system as the general reference system in biology. This book, first published in 1966, generated significant controversy and opened possibilities for evolutionary biology.

Oaks exemplify problems with the reproductive species concept which motivate a reconsideration of the use and nature of species. Ecology is important in the reconsideration. The species level is usually overemphasized in evolutionary thought; selection acts on phenotypes and any mutualistic units. Standard definitions tend to inhibit free conceptual progress. Multispecies, sets of broadly sympatric species that exchange genes, may occur among animals as well as plants and may conceivably bridge kingdoms. This phenomenon can be adaptively important. There may be (...) taxa without species. The degree of modality of adaptive zones can be investigated empirically. (shrink)

The Philosophy of Science, if the phrase were to be understood in the comprehensive sense which most naturally offers itself to our thoughts, ...

The Development of Modern Taxonomy Taxonomy has a long history, going back to the ancient Greeks and to forerunners even less sophisticated in systematics. Our interest here is centered on modern taxonomy itself, and we shall largely ...

Traditionally, species have been treated as classes. In fact they may be considered individuals. The logical term “individual” has been confused with a biological synonym for “organism.” If species are individuals, then: 1) their names are proper, 2) there cannot be instances of them, 3) they do not have defining properties, 4) their constituent organisms are parts, not members. “ Species " may be defined as the most extensive units in the natural economy such that reproductive competition occurs among their (...) parts. Species are to evolutionary theory as firms are to economic theory: this analogy resolves many issues, such as the problems of “reality” and the ontological status of nomenclatorial types. (shrink)

An enormous intellectual adventure. In this groundbreaking new book, the American biologist Edward O. Wilson, considered to be one of the world's greatest living scientists, argues for the fundamental unity of all knowledge and the need to search for consilience --the proof that everything in our world is organized in terms of a small number of fundamental natural laws that comprise the principles underlying every branch of learning. Professor Wilson, the pioneer of sociobiology and biodiversity, now once again breaks out (...) of the conventions of current thinking. He shows how and why our explosive rise in intellectual mastery of the truths of our universe has its roots in the ancient Greek concept of an intrinsic orderliness that governs our cosmos and the human species--a vision that found its apogee in the Age of Enlightenment, then gradually was lost in the increasing fragmentation and specialization of knowledge in the last two centuries. Drawing on the physical sciences and biology, anthropology, psychology, religion, philosophy, and the arts, Professor Wilson shows why the goals of the original Enlightenment are surging back to life, why they are reappearing on the very frontiers of science and humanistic scholarship, and how they are beginning to sketch themselves as the blueprint of our world as it most profoundly, elegantly, and excitingly is. (shrink)

The correct explanation of why species, in evolutionary theory, are individuals and not classes is the cladistic species concept. The cladistic species concept defines species as the group of organisms between two speciation events, or between one speciation event and one extinction event, or (for living species) that are descended from a speciation event. It is a theoretical concept, and therefore has the virtue of distinguishing clearly the theoretical nature of species from the practical criteria by which species may be (...) recognized at any one time. Ecological or biological (reproductive) criteria may help in the practical recognition of species. Ecological and biological species concepts are also needed to explain why cladistic species exist as distinct lineages, and to explain what exactly takes place during a speciation event. The ecological and biological species concepts work only as sub-theories of the cladistic species concept and if taken by themselves independently of cladism they are liable to blunder. The biological species concept neither provides a better explanation of species indivudualism than the ecological species concept, nor, taken by itself, can the biological species concept even be reconciled with species individualism. Taking the individuality of species seriously requires subordinating the biological, to the cladistic, species concept. (shrink)

The goal of a phylogenetic species concept is to reveal the smallest units that are analysable by cladistic methods and interpretable as the result of phylogenctic history. We define species as the smallest aggregation of populations (sexual) or lineagcs (asexual) diagnosable by a unique combination of character states in comparable individuals (semaphoronts). A character state is an inherited attribute distributed among all comparable individuals (semaphoronts) of the same historical population, clade, or terminal lineage. This definition of species is character-based and (...) pattern oriented. Evolutionary explanations of phylogenetic species are consistent with contemporary explanations of processes of speciation, but require only the assumption of nested hierarchical pattern. We discuss the compatibility of the phylogenetic species concept with various biological needs for species and justify its use at the exclusion of alternative species concepts. (shrink)