Despite the amount of work that has been produced on the subject over the years, the ‘transformation of cladistics’ is still a misunderstood episode in the history of comparative biology. Here, I analyze two outstanding, highly contrasting historiographic accounts on the matter, under the perspective of an influential dichotomy in the philosophy of science: the opposition between Scientific Realism and Empiricism. Placing special emphasis on the notion of ‘causal grounding’ of morphological characters in modern developmental biology’s theories, I arrive at (...) the conclusion that a ‘new transformation of cladistics’ is philosophically plausible. This ‘reformed’ understanding of ‘pattern cladistics’ entails retaining the interpretation of cladograms as ‘schemes of synapomorphies’, but in association to construing cladogram nodes as ‘developmental-genetic taxic homologies’, instead of ‘standard Darwinian ancestors’. The reinterpretation of pattern cladistics presented here additionally proposes to take Bas Van Fraassen’s ‘constructive empiricism’ as a philosophical stance that could properly support such analysis of developmental-genetic data for systematic purposes. The latter suggestion is justified through a reappraisal of previous ideas developed by prominent pattern cladists , which concerned a scientifically efficient ‘observable/non-observable distinction’ linked to the conceptual pair ‘ontogeny and phylogeny’. Finally, I argue that a robust articulation of Antirealist alternatives in systematics may provide a rational basis for its disciplinary separation from evolutionary biology, as well as for a critical reconsideration of the proper role of certain Scientific Realist positions, currently popular in comparative biology. (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)

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)

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 central to biology, but there is currently no agreement on what the adequate species concept should be, and many have adopted a pluralist stance: different species concepts will be required for different purposes. This thesis is a multidimensional analysis of species pluralism. First I explicate how pluralism differs monism and relativism. I then consider the history of species pluralism. I argue that we must re-frame the species problem, and that re-evaluating Aristotle's role in the histories of systematics can (...) shed light on pluralism. Next I consider different forms of pluralism: evolutionary and extra-evolutionary species pluralism, which differ in their stance on evolutionary theory. I show that pluralism is more than a debate about the species category, but a debate about which concepts are legitimate and a claim about how they interact with one another. Following that, I consider what sort of ontology is required for different forms of species pluralism. I argue that pluralists who deny the unity of biology will require a further plurality of frameworks, while those that ground their pluralism in evolution need only one framework. Finally, I consider what pluralism means for biological practice. I argue that species concepts are tools, and reflect on how pluralism can illuminate the way systematists approach the discovery of new species of yeast. Pluralism can make sense of the way species concepts are used, and can be developed to aid researchers in thinking about how to use the right tools for the right jobs. (shrink)

The longstanding species problem in biology has a history that suggests a solution, and that history is not the received history found in many texts written by biologists or philosophers. The notion of species as the division into subordinate groups of any generic predicate was the staple of logic from Aristotle through the middle ages until quite recently. However, the biological species concept during the same period was at first subtly and then overtly different. Unlike the logic sense, which relied (...) on definitions of the essence of both genus and species, biological species from the time of Epicurus were consistently considered to involve a reproductive element: in short, living species relied not on essential definitions, but on the generative cause, which might not be definable. I term this the generative conception of species: species were the generation by reproduction of form. This undercuts the claim that species before Darwin were essentialist, and divorces the notion of a type from that of essence. In fact, as late as the end of the nineteenth century, logicians explicitly treated biological “species” as a homonym only of logical essentialist species, and permitted considerable deviation from the type or form. At every point, species in logic were thought to be a subset, in effect, of some more general notion. I sketch a history of both philosophical and biological traditions of the species concept, before turning to the current conceptions. These are reconsidered in the light of this history, and in particular Mayr’s changing views are shown to be somewhat Whiggish, historiographically. Of the many touted biological species concepts, only one of which (Mayr’s) is called _the_ Biological Species Concept, none appears to capture all the relevant facts, intuitions, and operational requirements of biology. Cladistic conceptions, however, have much in common with the older philosophical literature, in that the natural group of cladism is the clade, or monophyletic group. After considering the Individuality Thesis, and the metaphysics of species, we see that species are the most particular terminal taxa in a clade, and that they are “defined” in terms of the particular synapomorphies, or evolved characters, that are causally responsible for keeping the lineages that organisms form distinct from one another. In this way, we can remain within the generative conception of species that has been in play for over two millennia, and yet avoid the pitfalls of prior attempts to find a universal conception of species. (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)