1 Integrative Biology 200A "PRINCIPLES OF PHYLOGENETICS" Spring 2008 University of California, Berkeley B.D. Mishler March 11, 2008: Species Concepts I. Importance of the species problem a. nomenclatorial requirements (all organisms must belong to a species). b. practicality -- need to organize diversity, summarize information, communicate, give names to things. c. legal issues -- endangered species legislation; conservation c. connection to evolutionary theory -- desire to have species as units functioning in process theories (but which process theories? how to connect units and theories without circularity?) d. philosophical concerns -- need to be clear about properties of units: sets vs. individuals, universalism vs. pluralism. II. Quasi-historical outline: a. typological or essentialist approach (i.e., systematics through Linnaeus) b. phenetic, morphological, or "natural" approach - older botanists (Gray, Bentham, Hooker) plus many recent botanists (Cronquist, Levin, Sokal & Crovello) - some recent cladists (!) (Nelson & Platnick, Cracraft, Nixon & Wheeler) c. "biological" species concept: interbreeding groups - classic isolation approach (most zoologists, e.g., Mayr, Dobzhansky) - newer recognition approach (some zoologists, see Paterson) d. "evolutionary" species concept: lineages (Simpson, Wiley) e. "ecological" species concept: niches (Van Valen) f. "species as individual": integrated, cohesive units with spatio-temporal boundaries (Ghiselin, Hull) g. "phylogenetic" species concept: basal monophyletic groups (will return later)2 III. Reason for the existence of a species problem: a. most of the above concepts and criteria conflict in most real cases -- different concepts (and processes) "pick out" different groups in each particular case, thus the implied correspondence between different criteria relied on by the BSC (and phenetic concepts) is abundantly falsified. b. operationality -- how to apply various concepts in a practical sense. c. what causes integration/cohesion of species? -- concerns: - breeding relationships are often clinal and/or non-transitive (what does "potential" interbreeding mean?) - gene flow is often very limited or lacking (what causes the evident distinctness of many asexual species?) - what is a niche? - developmental constraints (phylogenetic inertia)? d. what are the spatio-temporal boundaries of species? - monophyly? - origin? - extinction? IV. The winning argument for phylogenetic classification (review) The debate over classification has a long and checkered history (see Hull 1988; Stevens, 1994). A conceptual upheaval in the 1970's and 80's resulted in a true scientic revolution --Hennigian Phylogenetic Systematics. Many issues were at stake in that era, foremost of which was the nature of taxa. Are they just convenient groupings of organisms with similar features, or are they lineages, marked by homologies? A general, if not completely universal consensus has been reached, that taxa are (or at least should be) the latter (Hennig, 1966; Nelson, 1973; Farris, 1983; Sober, 1988). A summary of the arguments for why formal taxonomic names should be used solely to represent phylogenetic groups is as follows: evolution is the single most powerful and general process underlying biological diversity. The major outcome of the evolutionary process is the production of an ever-branching phylogenetic tree, through descent with modification along the branches. This results in life being organized as a hierarchy of nested monophyletic groups. Since the most effective and natural classification systems are those that "capture" entities resulting from processes generating the things being classified, the general biological classification system should be used to reflect the tree of life. This isn't to say that phylogeny is the only important organizing principle in biology, There are many ways of classifying organisms into a hierarchy, because of the many biological processes impinging on organisms. Many kinds of non-phylogenetic biological groupings are unquestionably useful for special purposes (e.g., "producers," "rain forests," "hummingbird pollinated plants," "bacteria"). However, it is generally agreed that there should be one consistent, general-purpose, reference system, for which the Linnaean hierarchy should be reserved. Phylogeny is the best criterion for the general purpose classification, both theoretically3 (the tree of life is the single universal outcome of the evolutionary process) and practically (phylogenetic relationship is the best criterion for summarizing known data about attributes of organisms and predicting unknown attributes). The other possible ways to classify can of course be used simultaneously, but should be regarded as special purpose classifications and clearly distinguished from phylogenetic formal taxa. Phylogenetic classification in detail: 1. Three ways of defining a name: Node-, Stem-, or Apomorphy-based. 2. Different ways of defining monophyly: synchronic (i.e., " all and only descendants of a common ancestor") or diachronic (i.e., " an ancestor and all of its descendants"). Which is better? Should the word "species" appear in the definition of monophyly? Does it matter? 3. Clade versus Lineage (see below for illustration). They are not the same thing -- "clade" is a synchronic concept, a snapshot of a lineage -- while a "lineage" is a diachronic concept, a series of replicators. V. A phylogenetic solution under the current codes of nomenclature Recognize that there is no species problem per se in systematics. Rather, there is a taxon problem. Once one has decided what taxon names are to represent in general, then species taxa should be the same kind of things -- just the least inclusive. The field of systematics in general has settled on restricting the use of formal taxonomic names to represent phylogenetically natural, monophyletic groups. So "species" should be the smallest one of those Grouping vs. ranking. There are two necessary parts to any species definition. The criteria by which organisms are grouped into taxa must be specified, as well as the criteria by which a taxon is ranked as a species rather than some other
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