This paper aims to illustrate one of the primary goals of the philosophy of biology⎯namely, the examination of central concepts in biological theory and practice⎯through an analysis of the concepts of population and metapopulation in evolutionary biology and ecology. I will first provide a brief background for my analysis, followed by a characterization of my proposed concepts: the causal interactionist concepts of population and metapopulation. I will then illustrate how the concepts apply to six cases that differ in their population (...) structure; this analysis will also serve to flesh out and defend the concepts a bit more. Finally, I will respond to some possible questions that my analysis may have raised and then conclude briefly. (shrink)

Millstein (2009) argues against conceptual pluralism with respect to the definition of “population,” and proposes her own definition of the term. I challenge both Millstein's negative arguments against conceptual pluralism and her positive proposal for a singular definition of population. The concept of population, I argue, does not refer to a natural kind; populations are constructs of biologists variably defined by contexts of inquiry.

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)

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

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

At least below the level of species, biological populations are not mind‐independent objects that scientists discover. Rather, biological populations are pragmatically constructed as objects of investigation according to the aims, interests, and values that inform particular research contexts. The relations among organisms that are constitutive of population‐level phenomena (e.g., mating propensity, genealogy, and competition) occur as matters of degree and so give rise to statistically defined open‐ended biological systems. These systems are rendered discrete units to satisfy practical needs and theoretical (...) preferences associated with specific contexts of investigation. While it may be possible to defend a realist position regarding biological relations among organisms, biological populations are “made” when contextual features determine which kinds and degrees of relations to privilege over others, and so how to bound genes in space and time. Consequently, the objectivity of population‐based approaches to species genome diversity cannot rest in the mind‐independence of populations themselves. (shrink)

Phylogenetic trees are meant to represent the genealogical history of life and apparently derive their justification from the existence of the tree of life and the fact that evolutionary processes are treelike. However, there are a number of problems for these assumptions. Here it is argued that once we understand the important role that phylogenetic trees play as models that contain idealizations, we can accept these criticisms and deny the reality of the tree while justifying the continued use of trees (...) in phylogenetic theory and preserving nearly all of what defenders of trees have called the “importance of tree thinking.”. (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)

This paper brings needed clarity to the influential view that species are cohesive entities held together by gene flow, and then develops an empirical argument against that view: Neglected data suggest gene flow is neither necessary nor sufficient for species cohesion. Implications are discussed. ‡I'm grateful to Rob Wilson, Alex Rueger and Lindley Darden for important comments on earlier drafts, and to Joseph Nagel, Heather Proctor, Ken Bond, members of the DC History and Philosophy of Biology reading group, and audience (...) members at the November 2006 meeting of the PSA, for helpful comments or discussion. Social Sciences and Humanities Research Council of Canada fellowship 752-2005-1208 supported research. †To contact the author, please write to: Philosophy Department, University of Wisconsin–Madison, 5185 Helen C. White Hall, 600 North Park Street, Madison, WI 53706; e-mail: [email protected]. (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)

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)

“Scientific theories are maps of the natural world.” This metaphor is often used as part of a deflationary argument for a weak but relatively global version of scientific realism, a version that recognizes the place of conventions, goals, and contingencies in scientific representations, while maintaining that they are typically true in a clear and literal sense. By examining, in a naturalistic way, some relationships between maps and what they map, we question the scope and value of realist construals of maps—and (...) by extension of scientific representations. Deflationary philosophy of science requires more variegated stances. (shrink)