At least three different issues are commonly referred to by the term “the species problem”: one concerns the necessary properties of species, a second the processes responsible for the existence of species, and a third methods for inferring species limits. Solutions have recently been proposed to the first two problems, which are conceptual in nature (the third is methodological). The first equates species with metapopulation lineages and proposes that existence as a separately evolving metapopulation lineage be considered the only necessary (...) property of species. The second views the species category as a cluster concept and proposes that no single process or set of processes be considered necessary for the existence of species. Although these two solutions have been portrayed as being in conflict, they are, in fact, highly compatible. Moreover, the proposals in question clarify the problem concerning methods for inferring the limits of species, which has for a long time been confused with the problem concerning the necessary properties of species. Together these proposals provide the opportunity for biology to move beyond debates about the definition of the species category and focus on estimating the boundaries and numbers of species as well as studying the diverse processes involved in their origin and persistence. BioEssays 27:1263–1269, 2005. © 2005 Wiley Periodicals, Inc. (shrink)

The theory of evolution, which provides the conceptual framework for all modern research in organismal biology and informs research in molecular bi- ology, has gone through several stages of expansion and refinement. Darwin and Wallace (1858) of course proposed the original idea, centering on the twin concepts of natural selection and common descent. Shortly thereafter, Wallace and August Weismann worked toward the complete elimination of any Lamarckian vestiges from the theory, leaning in particular on Weismann’s (1893) concept of the separation (...) of soma and germ, resulting in what is some- times referred to as “neo-Darwinism”. (shrink)

We argue that C. Darwin and more recently W. Hennig worked at times under the simplifying assumption of an eternal biosphere. So motivated, we explicitly consider the consequences which follow mathematically from this assumption, and the infinite graphs it leads to. This assumption admits certain clusters of organisms which have some ideal theoretical properties of species, shining some light onto the species problem. We prove a dualization of a law of T.A. Knight and C. Darwin, and sketch a decomposition result (...) involving the internodons of D. Kornet, J. Metz and H. Schellinx. A further goal of this paper is to respond to B. Sturmfels’ question, “Can biology lead to new theorems?”. (shrink)

Following Mayr (1961) evolutionary biologists often maintain that the hallmark of biology is its evolutionary perspective. In this view, biologists distinguish themselves from other natural scientists by their emphasis on why-questions. Why-questions are legitimate in biology but not in other natural sciences because of the selective character of the process by means of which living objects acquire their characteristics. For that reason, why-questions should be answered in terms of natural selection. Functional biology is seen as a reductionist science that applies (...) physics and chemistry to answer how-questions but lacks a biological point of view of its own. In this paper I dispute this image of functional biology. A close look at the kinds of issues studied in biology and at the way in which these issues are studied shows that functional biology employs a distinctive biological perspective that is not rooted in selection. This functional perspective is characterized by its concern with the requirements of the life-state and the way in which these are met. (shrink)

Internodons are a formalization of Hennig's concept of species. We present an alternative construction of internodons imposing a tree structure on the genealogical network. We prove that the segments (trivial unary trees) from this tree structure are precisely the internodons. We obtain the following spin-offs. First, the generated tree turns out to be an organismal tree of life. Second, this organismal tree is homeomorphic to the phylogenetic Hennigian species tree of life, implying the discovery of a multi-level tree of life: (...) this phylogenetic tree can be obtained by zooming out from the organismal tree, or conversely, the organismal tree of life can be generated by expanding the phylogenetic nodes into unary trees. Finally, the definition of the organismal tree allows an efficient algorithmic transformation of a given genealogical network into its corresponding phylogenetic species tree of life. The latter will be presented in a separate paper. (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)

This paper examines the species problem in microbiology and its implications for the species problem more generally. Given the different meanings of ‘species’ in microbiology, the use of ‘species’ in biology is more multifarious and problematic than commonly recognized. So much so, that recent work in microbial systematics casts doubt on the existence of a prokaryote species category in nature. It also casts doubt on the existence of a general species category for all of life (one that includes both prokaryotes (...) and eukaryotes). Prokaryote biology also undermines recent attempts to save the species category, such as the suggestion that species are metapopulation lineages and the idea that ‘species’ is a family resemblance concept. (shrink)

The architects of punctuated equilibrium and species selection as well as more recent workers (Vrba) have narrowed the original formulation of species selection and made it dependent upon so-called emergent characters. One criticism of this narrow version is the dearth of emergent characters with a consequent diminution in the robustness of species selection as an important evolutionary process. We argue that monomorphic species characters may at times be the focus of selection and that under these circumstances selection at the organism (...) level is by-passed due to the absence of critical variance. Selection therefore shifts to the species level where variability reemerges in a clade. The absence of critical variance among organisms prevents effect macroevolution from operating. If species-wide properties are important in macroevolutionary processes, as we contend, systematists should pay more attention to their elucidation. (shrink)

The circumscription of taxa and classification of organisms are fundamental tasks in the systematization of biological diversity. Their success depends on a unified idea concerning the species concept, evolution, and taxonomy; paradoxically, however, it requires a complete distinction between taxa and evolutionary units. To justify this view, I discuss these three topics of systematics. Species concepts are examined, and I propose a redefinition for the Taxonomic Species Concept based on nomenclatural properties, in which species are classes conventionally represented by a (...) binomial. Speciation is subsequently discussed, to demonstrate that concepts on the evolutionary process are damaged when species are considered as evolutionary units. Speciation should be considered a transition among patterns of a population and, consequently, always a sympatric process. This view contrasts with the majority of speciation models, which analyze cladogeneses and classify speciation geographically, usually considering allopatry the essential condition for the differentiation process. Finally, taxonomy is considered, to show that the equivalence between evolutionary and taxonomic units may also damage the practice of biological systematization. Principles and rules of nomenclature and classification should offer freedom to accommodate divergent opinions about systematics and to incorporate the evolution of knowledge; therefore, they should remain independent of biological theories. (shrink)

The circumscription of taxa and classification of organisms are fundamental tasks in the systematization of biological diversity. Their success depends on a unified idea concerning the species concept, evolution, and taxonomy; paradoxically, however, it requires a complete distinction between taxa and evolutionary units. To justify this view, I discuss these three topics of systematics. Species concepts are examined, and I propose a redefinition for the Taxonomic Species Concept based on nomenclatural properties, in which species are classes conventionally represented by a (...) binomial. Speciation is subsequently discussed, to demonstrate that concepts on the evolutionary process are damaged when species are considered as evolutionary units. Speciation should be considered a transition among patterns of a population and, consequently, always a sympatric process. This view contrasts with the majority of speciation models, which analyze cladogeneses and classify speciation geographically, usually considering allopatry the essential condition for the differentiation process. Finally, taxonomy is considered, to show that the equivalence between evolutionary and taxonomic units may also damage the practice of biological systematization. Principles and rules of nomenclature and classification should offer freedom to accommodate divergent opinions about systematics and to incorporate the evolution of knowledge; therefore, they should remain independent of biological theories. (shrink)

Species serve as both the basic units of macroevolutionary studies and as the basic units of taxonomic classification. In this paper I argue that the taxa identified as species by the Phylogenetic Species Concept (Mishler and Brandon 1987) are the units of biological organization most causally relevant to the evolutionary process but that such units exist at multiple levels within the hierarchy of any phylogenetic lineage. The PSC gives us no way of identifying one of these levels as the privileged (...) level on which taxonomic classifications can be based. (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)

There is no question that the constituents of cells and organisms are joined together by the part-whole relation. Genes are part of cells, and cells are part of organisms. Species taxa, however, have traditionally been conceived of, not as wholes with parts, but as classes with members. But why does the relation change abruptly from part-whole to class-membership above the level of organisms? Ghiselin, Hull and others have argued that it doesn't. Cells and organisms are cohesive mereological sums, and since (...) species taxa are like cells and organisms in the relevant respects, they, too, are cohesive mereological sums. I provide further reasons in support of the thesis that species are mereological sums. I argue, moreover, that the advocate of this thesis is committed to a form of pluralism with respect to the species concept. (shrink)

Pluralisms of various sorts are popular in philosophy of science, including those that imply some scientific concept x should be eliminated from science in favour of a plurality of concepts x1, x2, … xn. This article focuses on influential and representative arguments for such eliminative pluralism about the concept species. The main conclusions are that these arguments fail, that all other extant arguments also fail, and that this reveals a quite general dilemma, one that poses a defeasible presumption against many (...) eliminative pluralisms about various scientific concepts. The article ends by outlining a novel integrative alternative in defence of species. 1) Introduction 2) The species Concept, the Category ‘Species’, and the ‘Species’ Category Problem 3) What Are Eliminative Pluralism about species, and the Arguments for It? 4) Evaluation of Arguments 4.1 Splitting? 4.2 Lumping? 4.3 The eliminative pluralist’s dilemma 5) More General Lessons6Species Cohesion: An Integrative Alternative7Conclusion. (shrink)

A natural starting place for developing a phylogenetic species concept is to examine monophyletic groups of organisms. Proponents of “the” Phylogenetic Species Concept fall into one of two camps. The first camp denies that species even could be monophyletic and groups organisms using character traits. The second groups organisms using common ancestry and requires that species must be monophyletic. I argue that neither view is entirely correct. While monophyletic groups of organisms exist, they should not be equated with species. Instead, (...) species must meet the more restrictive criterion of being genealogically exclusive groups where the members are more closely related to each other than to anything outside the group. I carefully spell out different versions of what this might mean and arrive at a working definition of exclusivity that forms groups that can function within phylogenetic theory. I conclude by arguing that while a phylogenetic species concept must use exclusivity as a grouping criterion, a variety of ranking criteria are consistent with the requirement that species can be placed on phylogenetic trees. (shrink)

Whatever we take “life” to mean, it must involve an attempt to describe the objective reality beyond scientists’ biases. Traditionally, this is thought to involve comparing our scientific categories to “natural kinds.” But this approach has been tainted with an implicit metaphysics, inherited from Aristotle, that does not fit biological reality. In particular, we must accept that biological categories will never be specifiable in terms of necessary and sufficient conditions or shared underlying physical structures that produce clean boundaries. Biology blurs (...) all lines and failure to embrace this unique feature has blocked attempts to reach consensus on the meaning of “life.” Thus, while the three classical accounts all fall short of offering a complete definition, their advocates fail to realize that they share the same view of life’s ultimate, functional hallmark: its uniquely rich adaptive capacity. I develop an account of life as adaptive capacity that sidesteps debates about the relative importance of specific mechanisms and the precise location of boundaries to bring the three classical accounts together under a shared conceptual framework. (shrink)

Species in biology are traditionally perceived as kinds of organisms about which explanatory and predictive generalizations can be made, and biologists commonly use species in this manner. This perception of species is, however, in stark contrast with the currently accepted view that species are not kinds or classes at all, but individuals. In this paper I investigate the conditions under which the two views of species might be held simultaneously. Specifically, I ask whether upon acceptance of an ontology of species (...) as diachronic segments of the tree of life species can perform the epistemic role of kinds of organisms to which explanatory and predictive generalizations apply. I show that, for species-level segments of the tree of life, several requirements have to be met before the performance of this epistemic role is possible, and I argue that these requirements can be met by defining species according to the Composite Species Concept proposed by Kornet and McAllister in the 1990s. (shrink)

-/- 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)

Numerous concepts exist for biological species. This diversity of ideas derives from a number of sources ranging from investigative study of particular taxa and character sets to philosophical aptitude and world view to operationalism and nomenclatorial rules. While usually viewed as counterproductive, in reality these varied concepts can greatly enhance our efforts to discover and understand biological diversity. Moreover, this continued "turf war" and dilemma over species can be resolved if the various concepts are viewed in a hierarchical system and (...) each evaluated for its inherent level of consilience. Under this paradigm a theoretically appropriate, highly consilient concept of species capable of colligating the abundant types of species diversity offers the best guidance for developing and employing secondary operational concepts for identifying diversity. Of all the concepts currently recognized, only the non-operational Evolutionary Species Concept corresponds to the requisite parameters and, therefore, should serve as the theoretical concept appropriate for the category Species. As operational concepts, the remaining ideas have been incompatible with one another in their ability to encompass species diversity because each has restrictive criteria as to what qualifies as a species. However, the operational concepts can complement one another and do serve a vital role under the Evolutionary Species Concept as fundamental tools necessary for discovering diversity compatible with the primary theoretical concept. Thus, the proposed hierarchical system of primary and secondary concepts promises both the most productive framework for mutual respect for varied concepts and the most efficient and effective means for revealing species diversity. (shrink)