The so-called ‘‘species problem’’ has plagued evolution- ary biology since before Darwin’s publication of the aptly titled Origin of Species. Many biologists think the problem is just a matter of semantics; others complain that it will not be solved until we have more empirical data. Yet, we don’t seem to be able to escape discussing it and teaching seminars about it. In this paper, I briefly examine the main themes of the biological and philosophical liter- atures on the species problem, (...) focusing on identifying common threads as well as relevant differences. I then argue two fundamental points. First, the species problem is not primarily an empirical one, but it is rather fraught with philosophical questions that require—but cannot be settled by—empirical evidence. Second, the (dis-)solution lies in explicitly adopting Wittgenstein’s idea of ‘‘family resemblance’’ or cluster concepts, and to consider spe- cies as an example of such concepts. This solution has several attractive features, including bringing together apparently diverging themes of discussion among bio- logists and philosophers. The current proposal is con- ceptually independent (though not incompatible) with the pluralist approach to the species problem advocated by Mishler, Donoghue, Kitcher and Dupre ́, which implies that distinct aspects of the species question need to be emphasized depending on the goals of the researcher. From the biological literature, the concept of species that most closely matches the philosophical discussion pre- sented here is Templeton’s cohesion idea. (shrink)

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

The long-awaited revision of the industry standard on phylogenetics Since the publication of the first edition of this landmark volume more than twenty-five years ago, phylogenetic systematics has taken its place as the dominant paradigm of systematic biology. It has profoundly influenced the way scientists study evolution, and has seen many theoretical and technical advances as the field has continued to grow. It goes almost without saying that the next twenty-five years of phylogenetic research will prove as fascinating as the (...) first, with many exciting developments yet to come. This new edition of Phylogenetics captures the very essence of this rapidly evolving discipline. Written for the practicing systematist and phylogeneticist, it addresses both the philosophical and technical issues of the field, as well as surveys general practices in taxonomy. Major sections of the book deal with the nature of species and higher taxa, homology and characters, trees and tree graphs, and biogeography—the purpose being to develop biologically relevant species, character, tree, and biogeographic concepts that can be applied fruitfully to phylogenetics. The book then turns its focus to phylogenetic trees, including an in-depth guide to tree-building algorithms. Additional coverage includes: Parsimony and parsimony analysis Parametric phylogenetics including maximum likelihood and Bayesian approaches Phylogenetic classification Critiques of evolutionary taxonomy, phenetics, and transformed cladistics Specimen selection, field collecting, and curating Systematic publication and the rules of nomenclature Providing a thorough synthesis of the field, this important update to Phylogenetics is essential for students and researchers in the areas of evolutionary biology, molecular evolution, genetics and evolutionary genetics, paleontology, physical anthropology, and zoology. (shrink)

WE HAVE LEARNED in the preceding chapter that a revolutionary change of the species concept is in the making, a change which not only affects taxonomic procedure, but which also contributes considerably toward a better understanding of ...

Making Sense of Evolution explores contemporary evolutionary biology, focusing on the elements of theories—selection, adaptation, and species—that are complex and open to multiple possible interpretations, many of which are incompatible with one another and with other accepted practices in the discipline. Particular experimental methods, for example, may demand one understanding of “selection,” while the application of the same concept to another area of evolutionary biology could necessitate a very different definition.

Oaks exemplify problems with the reproductive species concept which motivate a reconsideration of the use and nature of species. Ecology is important in the reconsideration. The species level is usually overemphasized in evolutionary thought; selection acts on phenotypes and any mutualistic units. Standard definitions tend to inhibit free conceptual progress. Multispecies, sets of broadly sympatric species that exchange genes, may occur among animals as well as plants and may conceivably bridge kingdoms. This phenomenon can be adaptively important. There may be (...) taxa without species. The degree of modality of adaptive zones can be investigated empirically. (shrink)

The goal of a phylogenetic species concept is to reveal the smallest units that are analysable by cladistic methods and interpretable as the result of phylogenctic history. We define species as the smallest aggregation of populations (sexual) or lineagcs (asexual) diagnosable by a unique combination of character states in comparable individuals (semaphoronts). A character state is an inherited attribute distributed among all comparable individuals (semaphoronts) of the same historical population, clade, or terminal lineage. This definition of species is character-based and (...) pattern oriented. Evolutionary explanations of phylogenetic species are consistent with contemporary explanations of processes of speciation, but require only the assumption of nested hierarchical pattern. We discuss the compatibility of the phylogenetic species concept with various biological needs for species and justify its use at the exclusion of alternative species concepts. (shrink)

Geographic coincidence of animal and plant distributions to form recognizable patterns suggests that the separate components of the patterns are historically connected with each other and with geographic history. To seek evidence of these historical connections, cladograms of geographic areas, representing sequences of disruptive geologic, climatic, or geographic events, may be compared with biological cladograms, representing sequences of allopatric speciation events in relation to those geographic areas. Such comparisons, when they meet the minimum requirements of being among dichotomized threetaxon cladograms, (...) can resolve similar or dissimilar historical factors; two-taxon statements do not distinguish between groups with different histories. Congruence of biological and geological area-cladograms at a high confidence level (such as congruence of a five-taxon cladogram or four three-taxon cladograms with a geological cladogram, where the confidence level can be shown in cladistic theory to be 99%) means that specified events of paleogeography can be adopted as an explanation of the biological patterns. In such a cause and effect relationship, where the earth and its life are assumed to have evolved together, paleogeography is taken by logical necessity to be the independent variable and biological history, the dependent variable. Drawing a mathematical simile, the biological cladogram y (dependent variable), is a function of the geological cladogram x (independent variable), as in a simple regression of effect y on cause x where we are given no free choice as to which is the independent variable. Such a view implies that any specified sequence in earth history must coincide with some discoverable biological patterns; it does not imply a necessary converse that each biological pattern must coincide with some discoverable paleogeographic pattern, because some biological distributions might have resulted from stochastic processes (chance dispersal). Determining that all discoverable biological patterns conflict with a given corroborated or observed sequence of geologic, climatic, or geographic change (i.e., that y is not a function of x), in theory, therefore should falsify vicariance biogeography. Because dispersal biogeography presupposes stochastic processes, and any failure to meet the expectation of a postulated dispersal is explained by an additional dispersal, dispersal biogeography is immune to falsification. Without resort to paleontology or earth history, whether a given historical relationship implied by congruence of biological area-cladograms is the result of dispersal or vicariance can also be thought of in terms which minimize the number of necessary assumptions: did the sedentary organisms disperse with the vagile ones or did the vagile organisms vicariate with the sedentary ones? Cladistic congruence of a group of sedentary organisms with a group of vagile ones rejects dispersal for both. Hence, distributions of sedentary organisms have the potential to falsify dispersal theories as applied to vagile organisms, but distributions of vagile organisms cannot falsify vicariance theories as applied to sedentary ones. The problems that arise in various kinds of historical explanation are exemplified by several specific distributions of fishes and other organisms in North and Middle America and in the larger context of Pangaean history, and are discussed in relation to current species concepts. (shrink)