I defend a view of the species category, pluralistic realism, which is designed to do justice to the insights of many different groups of systematists. After arguing that species are sets and not individuals, I proceed to outline briefly some defects of the biological species concept. I draw the general moral that similar shortcomings arise for other popular views of the nature of species. These shortcomings arise because the legitimate interests of biology are diverse, and these diverse interests are reflected (...) in different legitimate approaches to the classification of organisms. In the final section, I show briefly how the pluralistic approach can help to illuminate some areas of biological and philosophical dispute. (shrink)

Many phylogenetic systematists have criticized the Biological Species Concept (BSC) because it distorts evolutionary history. While defenses against this particular criticism have been attempted, I argue that these responses are unsuccessful. In addition, I argue that the source of this problem leads to previously unappreciated, and deeper, fatal objections. These objections to the BSC also straightforwardly apply to other species concepts that are not defined by genealogical history. What is missing from many previous discussions is the fact that the Tree (...) of Life, which represents phylogenetic history, is independent of our choice of species concept. Some species concepts are consistent with species having unique positions on the Tree while others, including the BSC, are not. Since representing history is of primary importance in evolutionary biology, these problems lead to the conclusion that the BSC, along with many other species concepts, are unacceptable. If species are to be taxa used in phylogenetic inferences, we need a history-based species concept. (shrink)

I argue for accepting a pluralist approach to species, while rejecting the realism about species espoused by P. Kitcher and a number of other philosophers of biology. I develop an alternative view of species concepts as divisions of organisms into groups for study which are relative to the systematic explanatory interests of biologists at a particular time. I also show how this conception resolves a number of difficult puzzles which plague the application of particular species concepts.

The concept of individuality as applied to species, an important advance in the philosophy of evolutionary biology, is nevertheless in need of refinement. Four important subparts of this concept must be recognized: spatial boundaries, temporal boundaries, integration, and cohesion. Not all species necessarily meet all of these. Two very different types of pluralism have been advocated with respect to species, only one of which is satisfactory. An often unrecognized distinction between grouping and ranking components of any species concept is necessary. (...) A phylogenetic species concept is advocated that uses a grouping criterion of monophyly in a cladistic sense, and a ranking criterion based on those causal processes that are most important in producing and maintaining lineages in a particular case. Such causal processes can include actual interbreeding, selective constraints, and developmental canalization. The widespread use of the biological species concept is flawed for two reasons: because of a failure to distinguish grouping from ranking criteria and because of an unwarranted emphasis on the importance of interbreeding as a universal causal factor controlling evolutionary diversification. The potential to interbreed is not in itself a process; it is instead a result of a diversity of processes which result in shared selective environments and common developmental programs. These types of processes act in both sexual and asexual organisms, thus the phylogenetic species concept can reflect an underlying unity that the biological species concept can not. (shrink)

It is often said that there is just one “objective” tree of life: a single accurate branching hierarchy of species reflecting order of descent. For any two species, there is a single correct answer as to whether one is a “daughter” of the other, whether the two are “sister species” by virtue of their descent from a common parental species, whether they belong to a family line that excludes any given third species, and so on. The idea is intrinsically interesting. (...) It has consequences for what we should think about the evolutionary origins of Homo sapiens as well as other species.The idea also has important connections to the scientific discipline of systematics, which classifies organisms into related groups. The connection to systematics is what has made objectivity a topic of discussion for biologists and philosophers of biology. Cladism, now the dominant school of systematics, places organisms into groups depending just on their place in the tree of life. That is supposed to render classifica- tion objective. In section i, I recite claims to objectivity. In sections ii–v, I argue that the apparent objectivity is not what it seems to be. In section vi, I briefly revisit systematics. (shrink)

I defend a view of the species category, pluralistic realism, which is designed to do justice to the insights of many different groups of systematists. After arguing that species are sets and not individuals, I proceed to outline briefly some defects of the biological species concept. I draw the general moral that similar shortcomings arise for other popular views of the nature of species. These shortcomings arise because the legitimate interests of biology are diverse, and these diverse interests are reflected (...) in different legitimate approaches to the classification of organisms. In the final section, I show briefly how the pluralistic approach can help to illuminate some areas of biological and philosophical dispute. (shrink)

This paper takes up the cause of species pluralism. An argument for species pluralism is provided and standard monist objections to pluralism are answered. A new form of species pluralism is developed and shown to be an improvement over previous forms. This paper also offers a general foundation on which to base a pluralistic approach to biological classification.

With this manifesto, John Dupré systematically attacks the ideal of scientific unity by showing how its underlying assumptions are at odds with the central conclusions of science itself.

-/- Because species names play an important role in scientific communication, it is more important that species be understood to be taxa than that they be equated with functional ecological or evolutionary entities. Although most biologists would agree that taxa are composed of organisms that share a unique common history, 2 major challenges remain in developing a species-as-taxa concept. First, grouping: in the face of genealogical discordance at all levels in the taxonomic hierarchy, how can we understand the nature of (...) taxa? Second, ranking: what criteria should be used to designate certain taxa in a nested series as being species? The grouping problem can be solved by viewing taxa as exclusive groups of organisms— sets of organisms that form a clade for a plurality of the genome (more than any conflicting set). However, no single objective criterion of species rank can be proposed. Instead, the species rank should be assigned by practitioners based on the semisubjective application of a set of species-ranking criteria. Although these criteria can be designed to yield species taxa that approximately match the ecological, evolutionary, and morphological entities that taxonomists have traditionally associated with the species rank, such a correspondence cannot be enforced without undermining the assumption that species are taxa. The challenge and art of monography is to use genealogical and other kinds of data to assign all organisms to one and only one species-ranked taxon. Various implications of the species-as-ranked-taxa view are discussed, including the synchronic nature of taxa, fossil species, the treatment of hybrids, and species nomenclature. I conclude that, although challenges remain, adopting the view that species are ranked taxa will facilitate a much-needed revolution in taxonomy that will allow it to better serve the biodiversity informatic needs of the 21st century. (shrink)

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)

No question in theoretical biology has been more perennially controversial or perplexing than "What is a species?" Recent advances in phylogenetic theory have called into question traditional views of species and spawned many concepts that are currently competing for general acceptance. Once the subject of esoteric intellectual exercises, the "species problem" has emerged as a critically important aspect of global environmental concerns. Completion of an inventory of biodiversity, success in conservation, predictive knowledge about life on earth, management of material resources, (...) formulation of scientifically credible public policy and law, and more depend upon our adoption of the "right" species concept. Quentin D. Wheeler and Rudolf Meier present a debate among top systematic biology theorists to consider the strengths and weaknesses of five competing concepts. Debaters include (1) Ernst Mayr (Biological Species Concept), (2) Rudolf Meier and Rainer Willmann (Hennigian species concept), (3) Brent Mishler and Edward Theriot (one version of the Phylogenetic Species Concept), (4) Quentin Wheeler and Norman Platnick (a competing version of the Phylogenetic Species Concept), and (5) E. O. Wiley and Richard Mayden (the Evolutionary Species Concept). Each author or pair of authors contributes three essays to the debate: first, a position paper with an opening argument for their respective concept of species; second, a counterpoint view of the weakness of competing concepts; and, finally, a rebuttal of the attacks made by other authors. This unique and lively debate format makes the comparative advantages and disadvantages of competing species concepts clear and accessible in a single book for the first time, bringing to light numerous controversies in phylogenetic theory, taxonomy, and philosophy of science that are important to a wide audience. Species Concepts and Phylogenetic Theory will meet a need among scientists, conservationists, policy-makers, and students of biology for an explicit, critical evaluation of a large and complex literature on species. An important reference for professionals, the book will prove especially useful in classrooms and discussion groups where students may find a concise, lucid entrée to one of the most complex questions facing science and society. (shrink)

The renowned biologist and thinker Richard Dawkins presents his most expansive work yet: a comprehensive look at evolution, ranging from the latest developments in the field to his own provocative views. Loosely based on the form of Chaucer's Canterbury Tales, Dawkins's Tale takes us modern humans back through four billion years of life on our planet. As the pilgrimage progresses, we join with other organisms at the forty "rendezvous points" where we find a common ancestor. The band of pilgrims swells (...) into a vast crowd as we join first with other primates, then with other mammals, and so on back to the first primordial organism. Dawkins's brilliant, inventive approach allows us to view the connections between ourselves and all other life in a bracingly novel way. It also lets him shed bright new light on the most compelling aspects of evolutionary history and theory: sexual selection, speciation, convergent evolution, extinction, genetics, plate tectonics, geographical dispersal, and more. The Ancestor's Tale is at once a far-reaching survey of the latest, best thinking on biology and a fascinating history of life on Earth. Here Dawkins shows us how remarkable we are, how astonishing our history, and how intimate our relationship with the rest of the living world. (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.

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)

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)