Abstract Different concepts define species at the pattern-level grouping of organisms into discrete clusters, the level of the processes operating within and between populations leading to the formation and maintenance of these clusters, or the level of the inner-organismic genetic and molecular mechanisms that contribute to species cohesion or promote speciation. I argue that, unlike single-level approaches, a multi-level framework takes into account the complex sequences of cause-effect reinforcements leading to the formation and maintenance of various patterns, and allows for (...) revisions and refinements of pattern-based characterizations in light of the gradual elucidation of the causes and mechanisms contributing to pattern formation and maintenance. Content Type Journal Article Category Regular Article Pages 1-17 DOI 10.1007/s10441-011-9143-z Authors Tudor M. Baetu, Department of Philosophy, University of Maryland, 1125D Skinner Building, College Park, MD 20742, USA Journal Acta Biotheoretica Online ISSN 1572-8358 Print ISSN 0001-5342. (shrink)

Taxa and homologues can in our view be construed both as kinds and as individuals. However, the conceptualization of taxa as natural kinds in the sense of homeostatic property cluster kinds has been criticized by some systematists, as it seems that even such kinds cannot evolve due to their being homeostatic. We reply by arguing that the treatment of transformational and taxic homologies, respectively, as dynamic and static aspects of the same homeostatic property cluster kind represents a good perspective for (...) supporting the conceptualization of taxa as kinds. The focus on a phenomenon of homology based on causal processes (e.g., connectivity, activity-function, genetics, inheritance, and modularity) and implying relationship with modification yields a notion of natural kinds conforming to the phylogenetic-evolutionary framework. Nevertheless, homeostatic property cluster kinds in taxonomic and evolutionary practice must be rooted in the primacy of epistemological classification (homology as observational properties) over metaphysical generalization (series of transformation and common ancestry as unobservational processes). The perspective of individuating characters exclusively by historical-transformational independence instead of their developmental, structural, and functional independence fails to yield a sufficient practical interplay between theory and observation. Purely ontological and ostensional perspectives in evolution and phylogeny (e.g., an ideographic character concept and PhyloCode’s ‘individualism’ of clades) may be pragmatically contested in the case of urgent issues in biodiversity research, conservation, and systematics. (shrink)

Despite the traditional focus on metaphysical issues in discussions of natural kinds in biology, epistemological considerations are at least as important. By revisiting the debate as to whether taxa are kinds or individuals, I argue that both accounts are metaphysically compatible, but that one or the other approach can be pragmatically preferable depending on the epistemic context. Recent objections against construing species as homeostatic property cluster kinds are also addressed. The second part of the paper broadens the perspective by considering (...) homologues as another example of natural kinds, comparing them with analogues as functionally defined kinds. Given that there are various types of natural kinds, I discuss the different theoretical purposes served by diverse kind concepts, suggesting that there is no clear-cut distinction between natural kinds and other kinds, such as functional kinds. Rather than attempting to offer a unique metaphysical account of ‘natural’ kind, a more fruitful approach consists in the epistemological study of how different natural kind concepts are employed in scientific reasoning. (shrink)

Ernst Mayr's typological/population distinction is a conceptual thread that runs throughout much of his work in systematics, evolutionary biology, and the history and philosophy of biology. Mayr himself claims that typological thinking originated in the philosophy of Plato and that population thinking was first introduced by Charles Darwin and field naturalists. A more proximate origin of the typological/population thinking, however, is found in Mayr's own work on species. This paper traces the antecedents of the typological/population distinction by detailing Mayr's changing (...) views of species between 1942 and 1955. During this period, Mayr struggles to refine the biological species concept in the face of tensions that exist between studying species locally and studying them as geographically distributed collections of variable populations. The typological/population distinction is first formulated in 1955, when Mayr generalizes from the type concept versus the population concept in taxonomy to typological versus population thinking in biology more generally. Mayr's appeal to the more general distinction between typological and population thinking coincides with the waning status of natural history and evolutionary biology that occurs in the early 1950s and the distinction plays an important role in Mayr's efforts to legitimate the natural historical sciences. (shrink)

To cite this Article: Ereshefsky, Marc , 'Foundational Issues Concerning Taxa and Taxon Names', Systematic Biology, 56:2, 295 - 301 To link to this article: DOI: 10.1080/10635150701317401 URL: http://dx.doi.org/10.1080/10635150701317401..

Most biologists use the Linnaean system for constructing classifications of the organic world. The Linnaean system, however, has lost its theoretical basis due to the shift in biology from creationist and essentialist tenets to evolutionary theory. As a result, the Linnaean system is both cumbersome and ontologically vacuous. This paper illustrates the problems facing the Linnaean system, and ends with a brief introduction to an alternative approach to biological classification.

Homeostatic Property Cluster (HPC) theory suggests that species and other biological taxa consist of organisms that share certain similarities. HPC theory acknowledges the existence of Darwinian variation within biological taxa. The claim is that “homeostatic mechanisms” acting on the members of such taxa nonetheless ensure a significant cluster of similarities. The HPC theorist’s focus on individual similarities is inadequate to account for stable polymorphism within taxa, and fails properly to capture their historical nature. A better approach is to treat distributions (...) of traits in species populations as irreducible facts, explained in terms of selection pressures, genealogy, and other evolutionary factors. We call this view Population Structure Theory (PST). PST accommodates the view, implicit in biological systematics, that species are identified by reference to particular historical populations. (shrink)

In this paper I explore Aristotle’s views on natural kinds and the compatibility of pluralism and realism, a topic that has generated considerable interest among contemporary philosophers. I argue that, when it came to zoology, Aristotle denied that there is only one way of organizing the diversity of the living world into natural kinds that will yield a single, unified system of classification. Instead, living things can be grouped and regrouped into various cross-cutting kinds on the basis of objective similarities (...) and differences in ways that subserve the explanatory context. Since the explanatory aims of zoology are diverse and variegated, the kinds it recognizes must be equally diverse and variegated. At the same time, there are certain constraints on which kinds can be selected. And those constraints derive more from the causal structure of the world than from the proclivities of the classifier (hence the realism). This distinguishes Aristotle’s version of pluralistic realism from those contemporary versions (like Dupré’s “promiscuous realism”) that treat all or most classifications of a given domain as equally legitimate and not just a sub-set of kinds recognized by the science that studies it. By contrast, Aristotle privileges scientifically important kinds on the basis of their role in causal investigations. On this picture natural kinds are those kinds with the sort of causal structure that allows them to enter into scientific explanations. In the final section I argue that Aristotle’s zoology should remain of interest to philosophers and biologists alike insofar as it combines a pluralistic form of realism with a rank-free approach to classification. (shrink)

Cognitive definitions cannot accommodate fear as it occurs in species incapable of sophisticated cognition. Some think that fear must, therefore, be noncognitive. This paper explores another option, arguably more in line with evolutionary theory: that like other "biological universals" fear admits of variation across and within species. A paradigm case of such universals is species: it is argued that they can be defined by ostension in the manner of Putnam and Kripke without implying that they must have an invariable essence. (...) Emotions can be defined in this way too, in principle, but the theoretical understanding of homology necessary to do so is lacking at present. (shrink)

The purpose of this paper is to test the contemporary concept of biological species against some of the problems caused by treating species as spatiotemporally extended entities governed by criteria of persistence, identity, etc. After outlining the general problem of symmetric division in natural objects, I set out some useful distinctions (section 1) and confirm that species are not natural kinds (section 2). Section 3 takes up the separate issue of species definition, focusing on the Biological Species Concept (BSC). Sections (...) 4 and 5 examine the matter of species identity over space and time respectively, as determined by the BSC. Both gradualistic and punctuated equilibrium models of speciation are discussed. In section 6 I argue that the BSC fails to determine adequate criteria for dealing with certain kinds of speciation. Section 7 moves speculatively beyond the BSC to a brief examination of alternatives. (shrink)

The vision of natural kinds that is most common in the modern philosophy of biology, particularly with respect to the question whether species and other taxa are natural kinds, is based on a revision of the notion by Mill in A System of Logic. However, there was another conception that Whewell had previously captured well, which taxonomists have always employed, of kinds as being types that need not have necessary and sufficient characters and properties, or essences. These competing views employ (...) different approaches to scientific methodologies: Mill’s class-kinds are not formed by induction but by deduction, while Whewell’s type-kinds are inductive. More recently, phylogenetic kinds (clades, or monophyletic-kinds) are inductively projectible, and escape Mill’s strictures. Mill’s version represents a shift in the notions of kinds from the biological to the physical sciences. (shrink)

Defining Species: A Sourcebook from Antiquity to Today provides excerpts and commentary on the definition of «species from source material ranging from the ...

"--Joel Cracraft, American Museum of Natural History "This is not the potted history that one usually finds in texts and review articles.

Essentialism is widely regarded as a mistaken view of biological kinds, such as species. After recounting why (sections 2-3), we provide a brief survey of the chief responses to the “death of essentialism” in the philosophy of biology (section 4). We then develop one of these responses, the claim that biological kinds are homeostatic property clusters (sections 5-6) illustrating this view with several novel examples (section 7). Although this view was first expressed 20 years ago, and has received recent discussion (...) and critique, it remains underdeveloped and is often misrepresented by its critics (section 8). (shrink)

Although Bayesian methods are widely used in phylogenetic systematics today, the foundations of this methodology are still debated among both biologists and philosophers. The Bayesian approach to phylogenetic inference requires the assignment of prior probabilities to phylogenetic trees. As in other applications of Bayesian epistemology, the question of whether there is an objective way to assign these prior probabilities is a contested issue. This paper discusses the strategy of constraining the prior probabilities of phylogenetic trees by means of the Principal (...) Principle. In particular, I discuss a proposal due to Velasco (Biol Philos 23:455–473, 2008) of assigning prior probabilities to tree topologies based on the Yule process. By invoking the Principal Principle I argue that prior probabilities of tree topologies should rather be assigned a weighted mixture of probability distributions based on Pinelis’ (P Roy Soc Lond B Bio 270:1425–1431, 2003) multi-rate branching process including both the Yule distribution and the uniform distribution. However, I argue that this solves the problem of the priors of phylogenetic trees only in a weak form. (shrink)

There is a certain measure of perplexity concerning the significance of endopolyploidy. It seems that this results from a narrow frame of reference from which investigators view the phenomenon; that is, a predilection for emphasizing the specialized functional aspect of endopolyploidy as it operates in species at the present time overrides any consideration of the rôle that this state may play in the life of a species in its encounter with the forces of natural selection either in the past or (...) in the future.There does not seem to be any obvious relationship between the degree of endopolyploidy that a species can exhibit and either its basic DNA content or the structure of its nucleus. The significance of endopolyploidy may reside not so much in any specialized function that the condition can support, but rather in the properties that are consequent upon the endopolyploid condition itself and which are distinct from those that apply to diploid cells. Some of the properties of the endopolyploid state, and examples of their manifestation in plants and animals, are discussed. The conclusion is that these properties have a potential that opens possibilities for new paths of development and serves as a factor upon which natural selection can operate. (shrink)

The vast majority of biological taxonomists use the Linnaean system when constructing classifications. Taxa are assigned Linnaean ranks and taxon names are devised according to the Linnaean rules of nomenclature. Unfortunately, the Linnaean system has become theoretically outdated. Moreover, its continued use causes a number of practical problems. This paper begins by sketching the ontological and practical problems facing the Linnaean system. Those problems are sufficiently pressing that alternative systems of classification should be investigated. A number of proposals for an (...) alternative system are introduced and evaluated. The best aspects of those proposals are brought together to form a post-Linnaean system, and a comparison of the Linnaean and post-Linnaean systems is conducted. The final section of this paper considers not only the theoretical reasons for replacing the Linnaean system, but also the practical feasibility of adopting an alternative system. (shrink)

To cite this Article: Ereshefsky, Marc , 'Foundational Issues Concerning Taxa and Taxon Names', Systematic Biology, 56:2, 295 - 301 To link to this article: DOI: 10.1080/10635150701317401 URL: http://dx.doi.org/10.1080/10635150701317401..

Most biologists use the Linnaean system for constructing classifications of the organic world. The Linnaean system, however, has lost its theoretical basis due to the shift in biology from creationist and essentialist tenets to evolutionary theory. As a result, the Linnaean system is both cumbersome and ontologically vacuous. This paper illustrates the problems facing the Linnaean system, and ends with a brief introduction to an alternative approach to biological classification.

Homeostatic Property Cluster (HPC) theory suggests that species and other biological taxa consist of organisms that share certain similarities. HPC theory acknowledges the existence of Darwinian variation within biological taxa. The claim is that “homeostatic mechanisms” acting on the members of such taxa nonetheless ensure a significant cluster of similarities. The HPC theorist’s focus on individual similarities is inadequate to account for stable polymorphism within taxa, and fails properly to capture their historical nature. A better approach is to treat distributions (...) of traits in species populations as irreducible facts, explained in terms of selection pressures, genealogy, and other evolutionary factors. We call this view Population Structure Theory (PST). PST accommodates the view, implicit in biological systematics, that species are identified by reference to particular historical populations. (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)

Species are the basis of the taxonomic scheme. They are the lowest taxonomic category that are used as units for describing biodiversity and evolution. In this contribution we discuss the current species concept for prokaryotes. Such organisms are considered to represent the widest diversity among living organisms. Species is currently circumscribed as follows: A prokaryotic species is a category that circumscribes a (preferably) genomically coherent group of individual isolates/strains sharing a high degree of similarity in (many) independent features, comparatively tested (...) under highly standardized conditions. Although the number of described prokaryotic species is underrepresented in the living world, this phylo-phenetic or polythetic species concept currently in use is considered to be pragmatic, operational and universally applicable and successfully used for identification processes. (shrink)

Deduction leads to causal explanation in phylogenetic inference when the evidence, the systematic character, is conceptualized as a transformation series. Also, the deductive entailment of modus tollens is satisfied when those kinds of events are operationalized as patristic difference. Arguments to the contrary are based largely on the premise that character-states are defined intensionally as objects, in terms of similarity relations. However, such relations leave biologists without epistemological access to the causal explanation and explanatory power of historical statements. Moreover, the (...) prediction-making to which those kinds of relations are limited in practice can lead to a category error—the mental conversion of an abstraction (the classes defined in terms of similarity relations) into a thing (such as an historical individual). The latter practices and problems characterize pattern cladistics, taxa being interpreted as homeostatic property cluster natural kinds, and other instrumentalist research programs. (shrink)

‘‘Adaptive radiation’’ is an evocative metaphor for explosive evolutionary divergence, which for over 100 years has given a powerful heuristic to countless scientists working on all types of organisms at all phylogenetic levels. However, success has come at the price of making ‘‘adaptive radiation’’ so vague that it can no longer reflect the detailed results yielded by powerful new phylogeny-based techniques that quantify continuous adaptive radiation variables such as speciation rate, phylogenetic tree shape, and morphological diversity. Attempts to shoehorn the (...) results of these techniques into categorical ‘‘adaptive radiation: yes/no’’ schemes lead to reification, in which arbitrary quantitative thresholds are regarded as real. Our account of the life cycle of metaphors in science suggests that it is time to exchange the spent metaphor for new concepts that better represent the full range of diversity, disparity, and speciation rate across all of life. (shrink)

An examination of the post-Darwinian history of biological taxonomy reveals an implicit assumption that the definitions of taxon names consist of lists of organismal traits. That assumption represents a failure to grant the concept of evolution a central role in taxonomy, and it causes conflicts between traditional methods of defining taxon names and evolutionary concepts of taxa. Phylogenetic definitions of taxon names (de Queiroz and Gauthier 1990) grant the concept of common ancestry a central role in the definitions of taxon (...) names and thus constitute an important step in the development of phylogenetic taxonomy. By treating phylogenetic relationships rather than organismal traits as necessary and sufficient properties, phylogenetic definitions remove conflicts between the definitions of taxon names and evolutionary concepts of taxa. The general method of definition represented by phylogenetic definitions of clade names can be applied to the names of other kinds of composite wholes, including populations and biological species. That the names of individuals (composite wholes) can be defined in terms of necessary and sufficient properties provides the foundation for a synthesis of seemingly incompatible positions held by contemporary individualists and essentialists concerning the nature of taxa and the definitions of taxon names. (shrink)

Ontological questions in biology have typically focused on the nature of species: what are species; how are they identified and individuated? There is an analogous, but much neglected concern: what are characters; how are they identified and individuated? Character individuation is significant because biological systematics relies on a parsimony principle to determine phylogeny and classify taxa, and the parsimony principle is usually interpreted to favor the phylogenetic hypothesis that requires the fewest changes in characters. But no character individuation principle identified (...) so far is adequate. For biological systematics we need a better way of conceiving characters. (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)

I attempt to raise questions regarding elements of systematics—primarily in the realm of phylogenetic reconstruction—in order to provoke discussion on the current state of affairs in this discipline, and also evolutionary biology in general: e.g., conceptions of homology and homoplasy, hypothesis testing, the nature of and objections to Hennigian “phylogenetic systematics”, and the schism between (neo)Darwinian descendants of the “modern evolutionary synthesis” and their supposed antagonists, cladists and punctuationalists.

The project of this chapter is to understand what a phylogenetic tree represents and to discuss some of the implications that this has for the practice of systematics. At least the first part of this task, if not both parts, might appear trivial – or perhaps better suited for a single page in a textbook rather than a scholarly research paper. But this would be a mistake. While the task of interpreting phylogenetic trees is often treated in this trivial way, (...) in fact their interpretation is tied to foundational conceptual questions at the heart of systematics – questions whose answers are hotly disputed. As I will argue, common practices for the interpretation and use of trees are actually in conflict and therefore some must be given up. Here I defend the view that unacceptable principles about species as units of phylogeny must be given up. According to the view that I will develop, all phylogenetic trees depict the history of populations. The branches on trees represent collections of population lineages through time and the splits represent population lineage splits. I will argue for this view by focusing on how we use phylogenetic trees for inferences about the evolutionary past. (shrink)

Bayesian methods have become among the most popular methods in phylogenetics, but theoretical opposition to this methodology remains. After providing an introduction to Bayesian theory in this context, I attempt to tackle the problem mentioned most often in the literature: the “problem of the priors”—how to assign prior probabilities to tree hypotheses. I first argue that a recent objection—that an appropriate assignment of priors is impossible—is based on a misunderstanding of what ignorance and bias are. I then consider different methods (...) of assigning prior probabilities to trees. I argue that priors need to be derived from an understanding of how distinct taxa have evolved and that the appropriate evolutionary model is captured by the Yule birth–death process. This process leads to a well-known statistical distribution over trees. Though further modifications may be necessary to model more complex aspects of the branching process, they must be modifications to parameters in an underlying Yule model. Ignoring these Yule priors commits a fallacy leading to mistaken inferences both about the trees themselves and about macroevolutionary processes more generally. (shrink)

A phylogeny that allows for lateral gene transfer (LGT) can be thought of as a strictly branching tree (all of whose branches are vertical) to which lateral branches have been added. Given that the goal of phylogenetics is to depict evolutionary history, we should look for the best supported phylogenetic network and not restrict ourselves to considering trees. However, the obvious extensions of popular tree-based methods such as maximum parsimony and maximum likelihood face a serious problem—if we judge networks by (...) fit to data alone, networks that have lateral branches will always fit the data at least as well as any network that restricts itself to vertical branches. This is analogous to the well-studied problem of overfitting data in the curve-fitting problem. Analogous problems often have analogous solutions and we propose to treat network inference as a case of model selection and use the Akaike Information Criterion (AIC). Strictly tree-like networks are more parsimonious than those that postulate lateral as well as vertical branches. This leads to the conclusion that we should not always infer LGT events whenever it would improve our fit-to-data, but should do so only when the improved fit is larger than the penalty for adding extra lateral branches. (shrink)

Speciation is an aspect of evolutionary biology that has received little philosophical attention apart from articles mainly by biologists such as Mayr (1988). The role of speciation as a terminus a quo for the individuality of species or in the context of punctuated equilibrium theory has been discussed, but not the nature of speciation events themselves. It is the task of this paper to attempt to bring speciation events into some kind of general scheme, based primarily upon the work of (...) Sergey Gavrilets on adaptive landscapes, using migration rate, or gene flow, as the primary scale, and concluding that adaptive and drift explanations are complementary rather than competing. I propose a distinction between intrinsic and extrinsic selection, and the notion of reproductive reach and argue that speciation modes should be discriminated in terms of gene flow, the nature of selection maintaining reproductive reach, and whether the predominant cause is selective or stochastic. I also suggest that the notion of an adaptive “quasispecies” for asexual species is the primitive notion of species, and that members of reproductively coherent sexual species are additionally coadapted to their mating partners. (shrink)

The biological species (biospecies) concept applies only to sexually reproducing species, which means that until sexual reproduction evolved, there were no biospecies. On the universal tree of life, biospecies concepts therefore apply only to a relatively small number of clades, notably plants andanimals. I argue that it is useful to treat the various ways of being a species (species modes) as traits of clades. By extension from biospecies to the other concepts intended to capture the natural realities of what keeps (...) taxa distinct, we can treat other modes as traits also, and so come to understand that theplurality of species concepts reflects the biological realities of monophyletic groups.We should expect that specialists in different organisms will tend to favour those concepts that best represent the intrinsic mechanisms that keep taxa distinct in their clades. I will address the question whether modes ofreproduction such as asexual and sexual reproduction are natural classes, given that they are paraphyletic in most clades. (shrink)

The cladistic species concept proposed by Ridley (1989) rests on an undefined notion of speciation and its meaning is thus indeterminate. If the cladistic concept is made determinate through the definition of speciation, then it reduces to a form of whatever species concept is implicit in the definition of speciation and fails to be a truly alternative species concept. The cladistic formalism advocated by Ridley is designed to ensure that species are monophyletic, that they are objectively real entities, and that (...) they are individuals. It is argued that species need not be monophyletic in order to be real entities, and that ancestor-descendant relations are not the only relations that confer individuality on entities. The species problem is recast in terms of a futile quest for a definition of that single kind of entity to which the term species should uniquely apply. (shrink)

Marc Ereshefsky argues that pluralism about species suggests that the species concept is not theoretically useful. It is to be abandoned in favor of several concrete species concepts that denote real categories. While accepting species pluralism, the present paper rejects eliminativism about the species category. It is argued that the species concept is important and that it is possible to make sense of a general species concept despite the existence of different concrete species concepts.

Ernst Mayr's typological/population distinction is a conceptual thread that runs throughout much of his work in systematics, evolutionary biology, and the history and philosophy of biology. Mayr himself claims that typological thinking originated in the philosophy of Plato and that population thinking was first introduced by Charles Darwin and field naturalists. A more proximate origin of the typological/population thinking, however, is found in Mayr's own work on species. This paper traces the antecedents of the typological/population distinction by detailing Mayr's changing (...) views of species between 1942 and 1955. During this period, Mayr struggles to refine the biological species concept in the face of tensions that exist between studying species locally and studying them as geographically distributed collections of variable populations. The typological/population distinction is first formulated in 1955, when Mayr generalizes from the type concept versus the population concept in taxonomy to typological versus population thinking in biology more generally. Mayr's appeal to the more general distinction between typological and population thinking coincides with the waning status of natural history and evolutionary biology that occurs in the early 1950s and the distinction plays an important role in Mayr's efforts to legitimate the natural historical sciences. (shrink)

Biologists and philosophers have long recognized the importance of species, yet species concepts serve two masters, evolutionary theory on the one hand and taxonomy on the other. Much of present-day evolutionary and systematic biology has confounded these two roles primarily through use of the biological species concept. Theories require entities that are real, discrete, irreducible, and comparable. Within the neo-Darwinian synthesis, however, biological species have been treated as real or subjectively delimited entities, discrete or nondiscrete, and they are often capable (...) of being decomposed into other, smaller units. Because of this, biological species are generally not comparable across different groups of organisms, which implies that the ontological structure of evolutionary theory requires modification. Some biologists, including proponents of the biological species concept, have argued that no species concept is universally applicable across all organisms. Such a view means, however, that the history of life cannot be embraced by a common theory of ancestry and descent if that theory uses species as its entities.These ontological and biological difficulties can be alleviated if species are defined in terms of evolutionary units. The latter are irreducible clusters of reproductively cohesive organisms that are diagnosably distinct from other such clusters. Unlike biological species, which can include two or more evolutionary units, these phylogenetic species are discrete entities in space and time and capable of being compared from one group to the next. (shrink)

Biologists and philosophers that debate the existence of the species category are split into two main camps. Some believe that the species category does not exist and that the term ‘species’ should be junked. Others believe that given new biological insights and the application of philosophical ideas, we can show that the species category does exist. This paper charts a position between skeptics and defenders of the species category. That position holds that the species category does not exist, yet those (...) taxa we call ‘species’ do exist. And, despite skepticism over the species category, there are pragmatic reasons to keep the word ‘species.’ This approach to the species category is far from new, for it is the one that Darwin suggested. Hence it is dubbed ‘Darwin’s solution to the species problem.’. (shrink)

Homeostatic Property Cluster (HPC) theory suggests that species and other biological taxa consist of organisms that share certain similarities. HPC theory acknowledges the existence of Darwinian variation within biological taxa. The claim is that “homeostatic mechanisms” acting on the members of such taxa nonetheless ensure a significant cluster of similarities. The HPC theorist’s focus on individual similarities is inadequate to account for stable polymorphism within taxa, and fails properly to capture their historical nature. A better approach is to treat distributions (...) of traits in species populations as irreducible facts, explained in terms of selection pressures, genealogy, and other evolutionary factors. We call this view Population Structure Theory (PST). PST accommodates the view, implicit in biological systematics, that species are identified by reference to particular historical populations. (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)

Integration (interaction among parts of an entity) is suggested to be necessary for individuality (contra, Metaphysics and the Origin of Species). A synchronic species is an integrated individual that can evolve as a unified whole; a diachronic lineage is a non-integrated historical entity that cannot evolve. Synchronic species and diachronic lineages are consequently suggested to be ontologically distinct entities, rather than alternative perspectives of the same underlying entity (contra Baum (1998), Syst. Biol. 47, 641–653; de Queiroz (1995), Endless Forms: Species (...) and Speciation, pp. 57–75; Genes, Categories and Species). Species concepts usually refer to either one or the other entity; for instance, the Biological Species Concept refers to synchronic species, whereas the Cladistic Species Concept refers to diachronic lineages. The debate over species concepts has often failed to recognise this distinction, resulting in invalid comparisons between definitions that attempt to delineate fundamentally different entities. (shrink)

What Is Biodiversity? is a theoretical and conceptual exploration of the biological world and how diversity is valued. Maclaurin and Sterelny explore not only the origins of the concept of biodiversity, but also how that concept has been shaped by ecology and more recently by conservation biology. They explain the different types of biodiversity important in evolutionary theory, developmental biology, ecology, morphology and taxonomy and conclude that biological heritage is rich in not just one biodiversity but many. Maclaurin and Sterelny (...) also explore the case for the conservation of these biodiversities using option value theory, a tool borrowed from economics. (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 purpose of this paper is to test the contemporary concept of biological species against some of the problems caused by treating species as spatiotemporally extended entities governed by criteria of persistence, identity, etc. After outlining the general problem of symmetric division in natural objects, I set out some useful distinctions (section 1) and confirm that species are not natural kinds (section 2). Section 3 takes up the separate issue of species definition, focusing on the Biological Species Concept (BSC). Sections (...) 4 and 5 examine the matter of species identity over space and time respectively, as determined by the BSC. Both gradualistic and punctuated equilibrium models of speciation are discussed. In section 6 I argue that the BSC fails to determine adequate criteria for dealing with certain kinds of speciation. Section 7 moves speculatively beyond the BSC to a brief examination of alternatives. (shrink)

The project of this chapter is to understand what a phylogenetic tree represents and to discuss some of the implications that this has for the practice of systematics. At least the first part of this task, if not both parts, might appear trivial – or perhaps better suited for a single page in a textbook rather than a scholarly research paper. But this would be a mistake. While the task of interpreting phylogenetic trees is often treated in this trivial way, (...) in fact their interpretation is tied to foundational conceptual questions at the heart of systematics – questions whose answers are hotly disputed. As I will argue, common practices for the interpretation and use of trees are actually in conflict and therefore some must be given up. Here I defend the view that unacceptable principles about species as units of phylogeny must be given up. According to the view that I will develop, all phylogenetic trees depict the history of populations. The branches on trees represent collections of population lineages through time and the splits represent population lineage splits. I will argue for this view by focusing on how we use phylogenetic trees for inferences about the evolutionary past. (shrink)

A common view is that species occupy a unique position on the Tree of Life. Evaluating this claim requires an understanding of what the Tree of Life represents. The Tree represents history, but there are at least three biological levels that are often said to have genealogies: species, organisms, and genes. Here I focus on defending the plausibility of a gene-based account of the Tree. This leads to an account of species that are determined by gene genealogies. On this view, (...) an exclusive group is a group of organisms that forms a clade for a higher proportion of the genome than any conflicting clade. Taxa occupy a unique position in what can be called the ‘primary concordance tree’. But each gene has its own historical ‘Tree of Life’. I conclude by arguing that both organismal pedigrees with their corresponding Tree as well as gene genealogies and their trees are objectively real and play important, but different, roles in biological practice. (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)

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)

Defining Species: A Sourcebook from Antiquity to Today provides excerpts and commentary on the definition of «species from source material ranging from the ...

"--Joel Cracraft, American Museum of Natural History "This is not the potted history that one usually finds in texts and review articles.

Species concepts for bacteria and other microbes are contentious, because they are often asexual. There is a Problem of Homogeneity: every mutation in an asexual lineage forms a new strain, of which all descendents are clones until a new mutation occurs. We should expect that asexual organisms would form a smear or continuum. What causes the internal homogeneity of asexual lineages, if they are in fact homogeneous? Is there a natural “species concept” for “microbes”? Two main concepts devised for metazoans (...) and metaphytes have been applied to bacteria. One is the Recombination Concept, a revised form of the Biological Species Concept in which the homogenizing mechanism is the sharing of genome fragments, somewhat akin to sexual recombination. The other is the Ecological Species Concept, in which the ecological niche is that which maintains lineages as cohesive. In this paper I will discuss these two concepts, and offer an underlying model that conjoins them, and consider the implications for species concepts in general. In short, my argument is that asexual species are instances of the most primitive and underived notion of species, which I will call “quasispecies”, following Eigen, and that sexual species are merely one derived kind of species. Moreover, I will argue that there is a continuum of recombination from simple viral models in which each strain is a clone, through to obligate recombination of 50% of the parents’ genome, and that consequently there is no sharp division between “microbial” and more familiar species. (shrink)

Speciation is an aspect of evolutionary biology that has received little philosophical attention apart from articles mainly by biologists such as Mayr (1988). The role of speciation as a terminus a quo for the individuality of species or in the context of punctuated equilibrium theory has been discussed, but not the nature of speciation events themselves. It is the task of this paper to attempt to bring speciation events into some kind of general scheme, based primarily upon the work of (...) Sergey Gavrilets on adaptive landscapes, using migration rate, or gene flow, as the primary scale, and concluding that adaptive and drift explanations are complementary rather than competing. I propose a distinction between intrinsic and extrinsic selection, and the notion of reproductive reach and argue that speciation modes should be discriminated in terms of gene flow, the nature of selection maintaining reproductive reach, and whether the predominant cause is selective or stochastic. I also suggest that the notion of an adaptive “quasispecies” for asexual species is the primitive notion of species, and that members of reproductively coherent sexual species are additionally coadapted to their mating partners. (shrink)

The biological species (biospecies) concept applies only to sexually reproducing species, which means that until sexual reproduction evolved, there were no biospecies. On the universal tree of life, biospecies concepts therefore apply only to a relatively small number of clades, notably plants andanimals. I argue that it is useful to treat the various ways of being a species (species modes) as traits of clades. By extension from biospecies to the other concepts intended to capture the natural realities of what keeps (...) taxa distinct, we can treat other modes as traits also, and so come to understand that theplurality of species concepts reflects the biological realities of monophyletic groups.We should expect that specialists in different organisms will tend to favour those concepts that best represent the intrinsic mechanisms that keep taxa distinct in their clades. I will address the question whether modes ofreproduction such as asexual and sexual reproduction are natural classes, given that they are paraphyletic in most clades. (shrink)

The cladistic species concept proposed by Ridley (1989) rests on an undefined notion of speciation and its meaning is thus indeterminate. If the cladistic concept is made determinate through the definition of speciation, then it reduces to a form of whatever species concept is implicit in the definition of speciation and fails to be a truly alternative species concept. The cladistic formalism advocated by Ridley is designed to ensure that species are monophyletic, that they are objectively real entities, and that (...) they are individuals. It is argued that species need not be monophyletic in order to be real entities, and that ancestor-descendant relations are not the only relations that confer individuality on entities. The species problem is recast in terms of a futile quest for a definition of that single kind of entity to which the term species should uniquely apply. (shrink)

A far-reaching and influential view in evolutionary biology claims that species are cohesive units held together by gene flow. Biologists have recognized empirical problems facing this view; after sharpening the expression of the view, we present novel conceptual problems for it. At the heart of these problems is a distinction between two importantly different concepts of cohesion, what we call integrative and response cohesion. Acknowledging the distinction problematizes both the explanandum of species cohesion and the explanans of gene flow that (...) are central to the view we discuss. We conclude by tracing four broader implications for the study and conceptualization of species. (shrink)

This paper explains the metaphysical implications of the view that species are individuals (SAI). I first clarify SAI in light of the separate distinctions between individuals and classes, particulars and universals, and abstract and concrete things. I then show why the standard arguments given in defense of SAI are not compelling. Nonetheless, the ontological status of species is linked to the traditional "species problem," in that certain species concepts do entail that species are individuals. I develop the idea that species (...) names are rigid designators and show how this provides additional motivation for SAI. (shrink)

Biologists and philosophers that debate the existence of the species category are split into two main camps. Some believe that the species category does not exist and that the term ‘species’ should be junked. Others believe that given new biological insights and the application of philosophical ideas, we can show that the species category does exist. This paper charts a position between skeptics and defenders of the species category. That position holds that the species category does not exist, yet those (...) taxa we call ‘species’ do exist. And, despite skepticism over the species category, there are pragmatic reasons to keep the word ‘species.’ This approach to the species category is far from new, for it is the one that Darwin suggested. Hence it is dubbed ‘Darwin’s solution to the species problem.’. (shrink)

Homeostatic Property Cluster (HPC) theory suggests that species and other biological taxa consist of organisms that share certain similarities. HPC theory acknowledges the existence of Darwinian variation within biological taxa. The claim is that “homeostatic mechanisms” acting on the members of such taxa nonetheless ensure a significant cluster of similarities. The HPC theorist’s focus on individual similarities is inadequate to account for stable polymorphism within taxa, and fails properly to capture their historical nature. A better approach is to treat distributions (...) of traits in species populations as irreducible facts, explained in terms of selection pressures, genealogy, and other evolutionary factors. We call this view Population Structure Theory (PST). PST accommodates the view, implicit in biological systematics, that species are identified by reference to particular historical populations. (shrink)

Species are the basis of the taxonomic scheme. They are the lowest taxonomic category that are used as units for describing biodiversity and evolution. In this contribution we discuss the current species concept for prokaryotes. Such organisms are considered to represent the widest diversity among living organisms. Species is currently circumscribed as follows: A prokaryotic species is a category that circumscribes a (preferably) genomically coherent group of individual isolates/strains sharing a high degree of similarity in (many) independent features, comparatively tested (...) under highly standardized conditions. Although the number of described prokaryotic species is underrepresented in the living world, this phylo-phenetic or polythetic species concept currently in use is considered to be pragmatic, operational and universally applicable and successfully used for identification processes. (shrink)

This is the final draft of a paper written for a collection in honour of Ruth Millikan. Millikan has argued that biological taxa are historical kinds. Her argument is puzzling: it shows only that biological taxa are relational. And this conclusion has been challenged by Michael Devitt. Here, I argue that stable polymorphisms in kinds require underlying mechanisms that keep sub-groups separate. (This answers a criticism of my earlier views by Wilson, Barker, and Brigandt.) I argue that this condition brings (...) in a kind of historicity that Millikan wants, but that a further kind of historicity is dubious. (shrink)

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 (monistic) grouping criterion of monophyly in a cladistic sense, and a (pluralistic) 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)

An examination of the post-Darwinian history of biological taxonomy reveals an implicit assumption that the definitions of taxon names consist of lists of organismal traits. That assumption represents a failure to grant the concept of evolution a central role in taxonomy, and it causes conflicts between traditional methods of defining taxon names and evolutionary concepts of taxa. Phylogenetic definitions of taxon names (de Queiroz and Gauthier 1990) grant the concept of common ancestry a central role in the definitions of taxon (...) names and thus constitute an important step in the development of phylogenetic taxonomy. By treating phylogenetic relationships rather than organismal traits as necessary and sufficient properties, phylogenetic definitions remove conflicts between the definitions of taxon names and evolutionary concepts of taxa. The general method of definition represented by phylogenetic definitions of clade names can be applied to the names of other kinds of composite wholes, including populations and biological species. That the names of individuals (composite wholes) can be defined in terms of necessary and sufficient properties provides the foundation for a synthesis of seemingly incompatible positions held by contemporary individualists and essentialists concerning the nature of taxa and the definitions of taxon names. (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 purpose of this paper is to test the contemporary concept of biological species against some of the problems caused by treating species as spatiotemporally extended entities governed by criteria of persistence, identity, etc. After outlining the general problem of symmetric division in natural objects, I set out some useful distinctions (section 1) and confirm that species are not natural kinds (section 2). Section 3 takes up the separate issue of species definition, focusing on the Biological Species Concept (BSC). Sections (...) 4 and 5 examine the matter of species identity over space and time respectively, as determined by the BSC. Both gradualistic and punctuated equilibrium models of speciation are discussed. In section 6 I argue that the BSC fails to determine adequate criteria for dealing with certain kinds of speciation. Section 7 moves speculatively beyond the BSC to a brief examination of alternatives. (shrink)

Defining Species: A Sourcebook from Antiquity to Today provides excerpts and commentary on the definition of «species from source material ranging from the ...

"--Joel Cracraft, American Museum of Natural History "This is not the potted history that one usually finds in texts and review articles.

The biological species (biospecies) concept applies only to sexually reproducing species, which means that until sexual reproduction evolved, there were no biospecies. On the universal tree of life, biospecies concepts therefore apply only to a relatively small number of clades, notably plants andanimals. I argue that it is useful to treat the various ways of being a species (species modes) as traits of clades. By extension from biospecies to the other concepts intended to capture the natural realities of what keeps (...) taxa distinct, we can treat other modes as traits also, and so come to understand that theplurality of species concepts reflects the biological realities of monophyletic groups.We should expect that specialists in different organisms will tend to favour those concepts that best represent the intrinsic mechanisms that keep taxa distinct in their clades. I will address the question whether modes ofreproduction such as asexual and sexual reproduction are natural classes, given that they are paraphyletic in most clades. (shrink)