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For Peer Review Only For peer review only. Do not cite. Species as Ranked Taxa Journal: Systematic Biology Manuscript ID: USYB-2008-130.R2 Manuscript Type: Regular Manuscript Date Submitted by the Author: n/a Complete List of Authors: Baum, David; University of Wisconsin, Botany Keywords: Concordance, Exclusivity, Gene genealogy, Hybridization, Monography, Phylogenetic nomenclature, Species concepts, Taxonomy http://mc.manuscriptcentral.com/systbiolSystematic BiologyFor Peer Review Only RUNNING HEAD: SPECIES AS RANKED TAXA Species as Ranked Taxa DAVID A. BAUM Department of Botany, University of Wisconsin – Madison, 430 Lincoln Dr., Madison WI 53706, USA: [email protected] Contact Information: David A. Baum Dept. of Botany 430 Lincoln Dr. Madison WI 53706 Email: [email protected] Tel: (608)265-5385Page 1 of 44http://mc.manuscriptcentral.com/systbiolSystematic Biology123456789101112131415161718192021222324252627282930313233343536373839404142434445464748495051525354555657585960For Peer Review Only Page 2 Abstract:— 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. While most biologists would agree that taxa are composed of organisms that share a unique common history, two 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 semi-subjective application of a set of species-ranking criteria. While 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, while 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. KEYWORDS: Concordance; Exclusivity; Gene genealogy; Hybridization; Monography; Phylogenetic nomenclature; Species concepts; TaxonomyPage 2 of 44http://mc.manuscriptcentral.com/systbiolSystematic Biology123456789101112131415161718192021222324252627282930313233343536373839404142434445464748495051525354555657585960For Peer Review Only Page 3 Considering that species level taxonomy provides the basic reference system for biological diversity, it is unfortunate that biologists have failed to establish an agreed upon meaning of the term “species.” Calling a group of organisms a species might be taken to mean that it is an evolutionary unit, a lineage, a population, an ecological entity, a morphologically distinct entity, or just a group given a formal binomial name. One could argue that such imprecision over the meaning of species is to be expected and is not undesirable when meaning is established by “language games” (Pigliucci, 2003). This perspective implies that the species category is a cluster concept, referring to a set of entities that share a “family resemblance” rather than being tied to any necessary and sufficient attributes. Even if one thinks that family resemblance is the way that meaning is established in everyday discourse, in the context of rigorous scientific communication we can aspire to more precision. But given the range of connotations of the term, how can we settle on a set of necessary and sufficient properties of “species?” Although a broad diversity of species concepts have been proposed, I would suggest that there is one major axis of variation: species-as-taxa versus species-as-functional-units. Species-as-taxon concepts are ones that emphasize the similarities between species and taxa at other ranks and mainly reflect a desire to guide taxonomists in the practice of assigning groups of organisms to species taxa. Species-as-functional-units concepts are ones that emphasize the functional cohesion or causal efficacy of species and generally emphasize the role of the term “species” in evolutionary and ecological theory. The clearest way to distinguish these two kinds of concepts is by asking the question: What is it about a group of organisms living at one moment that would make them one species as to opposed to two, or many, or a subset of a single species? If the answer is something about their functional integrity (for example interbreeding potential) or ecological cohesion then the concept is “functional.” By this reasoning the Page 3 of 44http://mc.manuscriptcentral.com/systbiolSystematic Biology123456789101112131415161718192021222324252627282930313233343536373839404142434445464748495051525354555657585960For Peer Review Only Page 4 biological (Mayr, 1969), evolutionary (Simpson, 1961; Wiley, 1978), ecological (Van Valen, 1976), and cohesion (Templeton, 1989) species concepts are all functional in outlook. If the answer to the question stresses the same kinds of attributes that are used to delimit higher taxa, then the species concept is taxic in outlook. Thus, the phenetic (Sneath, 1976), morphological (Cronquist, 1978), diagnosability (Cracraft, 1983; Nixon and Wheeler, 1990; Davis and Nixon, 1992); monophyly (de Queiroz and Donoghue, 1988), and genealogical (Baum and Shaw, 1995) concepts all use the same grouping criterion for species and higher taxa, making them species-as-taxa concepts. However, some other concepts require some exploration. The internodal or Hennigian species concept argues that


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UW-Madison BOTANY 563 - Species as Ranked Taxa

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