Quentin D. Wheeler

The intellectual content of taxonomy: a comment on DNA taxonomy

1 Tautz, D. et al. (2002) DNA points the way ahead in taxonomy. Nature 418, 479 2 Tautz, D. et al. (2003) A plea for DNA taxonomy. Trends Ecol. Evol. 18 DOI: 10.1016/S0169-5347(02)00041-1 3 Minelli, A. (2003) The status of taxonomic literature. Trends Ecol. Evol. 18 DOI: 10.1016/S0169-5347(02)00051-4 4 Knapp, S. et al. (2002) Taxonomy needs evolution, not revolution. Nature 419, 559 5 Godfray, H.C.J. (2002) Challenges for taxonomy. Nature 417, 17–19 6 Mallet, J. (2003) Taxonomy: renaissance or Tower of Babel? DOI: 10.1016/S0169-5347(02)00061-7 7 Lipscomb, D. et al. (2003) The intellectual content of taxonomy: a comment on DNA taxonomy. DOI: 10.1016/S0169-5347(02)00060-5

Taxonomic Impediment or Impediment to Taxonomy? A Commentary on Systematics and the Cybertaxonomic-Automation Paradigm

Marcelo R. de Carvalho AE Flavio A. Bockmann AE Dalton S. Amorim AE Carlos Roberto F. Brandao AE Mario de Vivo AE Jose L. de Figueiredo AE Heraldo A. Britski AE Mario C. C. de Pinna AE Naercio A. Menezes AE Fernando P. L. Marques AE Nelson Papavero AE Eliana M. Cancello AE Jorge V. Crisci AE John D. McEachran AE Robert C. Schelly AE John G. Lundberg AE Anthony C. Gill AE Ralf Britz AE Quentin D. Wheeler AE Melanie L. J. Stiassny AE Lynne R. Parenti AE Larry M. Page AE Ward C. Wheeler AE Julian Faivovich AE Richard P. Vari AE Lance Grande AE Chris J. Humphries AE Rob DeSalle AE Malte C. Ebach AE Gareth J. Nelson

The illogical basis of phylogenetic nomenclature

The current advocacy for the so-called PhyloCode has a history rooted in twentieth-century arguments among biologists and philosophers regarding a putative distinction between classes and individuals. From this seemingly simple and innocuous discussion have come supposed distinctions between definitions and diagnosis, classification and systematization, and now Linnaean and “phylogenetic” nomenclature. Nevertheless, the metaphysical dichotomy of class versus individual, insofar as its standard applications to the issue of biological taxonomy are concerned, is an outdated remnant of early logical positivist thinking. Current views on natural kinds and their definitions under a scientific realist perspective provide grounds for rejecting the class versus individual dichotomy altogether insofar as biological entities are concerned. We review the role of natural kinds in scientific practice and the nature of definitions and scientific classifications. Although inherent instabilities of the PhyloCode are clearly sufficient to argue against the general application of this nominally phylogenetic system, our goal here is to address serious and fundamental flaws in its very foundation by exposing the unsubstantiated philosophical assumptions preceding and subtending it.ResumenLas propuestas actuales en favor del llamado Código de Nomenclatura Filogenética (Phylo-Code) tienen una historia basada en argumentos desarrollados, durante el siglo veinte, por biólogos y filósofos sobre una distinción putativa entre clases e individuos. De esta simple y aparentemente inocua discusión han surgido supuestas distinciones entre definición y diagnosis, clasificación y sistematización, y ahora entre nomenclatura Lineana y “filogenética.” Sin embargo, la dicotomía metafísica clase contra individuo, al menos en lo concerniente a su aplicación estándar al tema de taxonomía biológica, es un remanente obsoleto del pensamiento positivista lógico. Opiniones actuales sobre categorías naturales y sus definiciones bajo la perspectiva del realismo científico proveen bases para rechazar por completo dicha dicotomía, al menos en lo que concierne a las entidades biológicas. En este artículo se revisa el papel de las categorías naturales en la práctica científica, y la naturaleza de las definiciones y la clasificación científica. Aún cuando la inestabilidad inherente en el Código de Nomenclatura Filogenética es claramente suficiente para argumentar contra la aplicación general de este sistema nominal filogenético, el objetivo de este artículo es mostrar las serias y fundamentales deficiencias en sus propias bases al exponer las suposiciones filosóficas sin fundamento que le preceden y sustentan.

Mapping the biosphere: Exploring species to understand the origin, organization and sustainability of biodiversity

The time is ripe for a comprehensive mission to explore and document Earths species. This calls for a campaign to educate and inspire the next generation of professional and citizen species explorers, investments in cyber-infrastructure and collections to meet the unique needs of the producers and consumers of taxonomic information, and the formation and coordination of a multi-institutional, international, transdisciplinary community of researchers, scholars and engineers with the shared objective of creating a comprehensive inventory of species and detailed map of the biosphere. We conclude that an ambitious goal to describe 10 million species in less than 50 years is attainable based on the strength of 250 years of progress, worldwide collections, existing experts, technological innovation and collaborative teamwork. Existing digitization projects are overcoming obstacles of the past, facilitating collaboration and mobilizing literature, data, images and specimens through cyber technologies. Charting the biosphere is enormously complex, yet necessary expertise can be found through partnerships with engineers, information scientists, sociologists, ecologists, climate scientists, conservation biologists, industrial project managers and taxon specialists, from agrostologists to zoophytologists. Benefits to society of the proposed mission would be profound, immediate and enduring, from detection of early responses of flora and fauna to climate change to opening access to evolutionary designs for solutions to countless practical problems. The impacts on the biodiversity, environmental and evolutionary sciences would be transformative, from ecosystem models calibrated in detail to comprehensive understanding of the origin and evolution of life over its 3.8 billion year history. The resultant cyber-enabled taxonomy, or cybertaxonomy, would open access to biodiversity data to developing nations, assure access to reliable data about species, and change how scientists and citizens alike access, use and think about biological diversity information.

ANOTHER WAY OF LOOKING AT THE SPECIES PROBLEM: A REPLY TO DE QUEIROZ AND DONOGHUE

We found the recent paper on the relationship ofphylogenetics to the species problem by de Queiroz and Donoghue (1988) unnecessarily eclectic. We were puzzled when de Queiroz and Donoghue, as they said they would (p. 319), advocated “neither a new species concept nor any existing one”. Given a phylogenetic perspective, some species concepts are clearly preferable to others, just as parsimony is a preferable criterion to other possible ones for constructing cladograms. Compilations of ideas on a subject are not nearly so helpful as interpretations or syntheses of them. The use of monophyly, paraphyly, and polyphyly at the infraspecific level (de Queiroz and Donoghue, 1988: 319) is inaccurate. Hennig (1966: 73) made his intentions fully explicit, defining a monophyletic group as “a group of species descended from a single (‘stem’) species, and which includes all species descended from this stem species’’ (italics ours). We do not invoke Hennig here for authoritarian reasons. Hennig’s restricted use of the term monophyly was based on a clear and concise understanding of the differences between tokogenetic and phylogenetic relationships. Hennig (1966: 73) intended to group together “all descendants of a group of individuals that at their time belonged to a . . . single species”, and not those belonging to individual infraspecific populations. Species are the fundamental units of phylogenetic analysis, and monophyly is intended to describe situations of most recent common ancestry. Things less than species are the units for tokogenetic, not phylogenetic, study, and are better described in non-phylogenetic terminology. Similarly, paraphyly was not intended to apply to situations below the species level (Nelson, 1989). When a human gives birth, does she become paraphyletic? Because species are the smallest terms analysed by cladistic methods (Nelson, 1979) it is logically inconsistent to define them in a way that depends upon topological (cladistic) resolution. I t also follows that in cases where cladistic analysis is possible, as opposed to some kind of tokogenetic analysis, we are dealing with distinct species and not with infraspecific units. As we suggest elsewhere (Nixon and Wheeler, submitted), this distinction relates to the constancy of charactet. states of species versus the inconstancy of 1raiL.r ofindividuals or populations. Constancy, in this context, refers to the presence in all individuals of a terminal taxon of such states in the original or in some modified condition (Platnick, 1979; Nelson and Platnick, 1981). Thus, character constancy is not the absence of phenotypic variability. Backbone is a state shared by all animals termed vertebrates, yet the phenotypic expression of backbones is diverse. O n individuality, de Queiroz and Donoghue conclude that “according to Hull ( 1978) and Wiley (1981) individuals must not only be spatiotemporally localized but also must be continuous and cohesive”. The authors do not explicitly say so, but we presume their concurrence with Hull’s points from the fact that subheadings are devoted to continuity and cohesion. Under “continuity” the discussion reveals a confusion about what is and is not an

ONTOGENY AND CHARACTER PHYLOGENY

Abstract— The doctrine of recapitulation was long ago exchanged for a view that ontogeny is orderly and recapitulates ancestral ontogenies. Only recently has the pattern of ontogeny, as a means for determining individual character phylogenies (polarities), been explicitly explored by Gareth Nelson and other cladists. Constraints on outgroup comparisons are suggested to apply to Nelsons rule equally, and the supposed distinction between “direct” and “indirect” methods is suggested to be nonexistent. Nelsons rule is concluded to measure character adjacency directly, but polarity indirectly. Nelsons (ontogenetic) rule is compared to the Outgroup Rule of Watrous and Wheeler, based on 60 postembryonic larval characters of three species of slime‐mold beetles of the genus Agathidium (onisemdes Palisot de Beauvois, pulchrum LeConte, aristerium Wheeler), and reference to larvae of Amsotoma basalts (Le Conte) as an outgroup. Polarities were hypothesized based on each rule and cladograms constructed with the microcomputer programs Henning86 (J. S. Farris) and CLADOS (K. C. Nixon). With levels of analytical error, or homoplasy, measured as the consistency index, the results were compared and the least homoplastic solutions preferred. It is concluded that the outgroup rule and Nelsons rule arc of about the same efficacy as criteria for polarity, and that each is ultimately justified on the basis of parsimony. The following hypothesis of relationships is accepted for the species studied: (Anisotoma basalts + (Agathidium oniscoides + (Agathidium pulchrum + Agathidium arislerium))).

Impediments to taxonomy and users of taxonomy: accessibility and impact evaluation

There has been much discussion of the “taxonomic impediment”. This phrase confuses two kinds of impediment: an impediment to end users imposed by lack of reliable information; and impediments to taxonomy itself, which vary from insufficient funding to low citation rates of taxonomic monographs. In order to resolve both these types of impediment, taxonomy needs to be revitalized through funding and training taxonomists, as well as investing in taxonomic revisions and monographs rather than technological surrogates such as DNA barcoding.
© The Willi Hennig Society 2011.

Forum – Taxonomic Stability is Ignorance☆

Absolute nomenclatural stability is undesirable in phylogenetic classifications because they reflect changing hypotheses of cladistic relationships. De Queiroz and Gauthiers (1990:Syst. Zool.39, 307–322; 1992:A. Rev. Ecol. Syst.23, 449–480; 1994:Trends Ecol. Evol.9, 27–31) alternative to Linnaean nomenclature is concluded to provide stable names for unstable concepts. In terms of communicating either characters shared by species of a named taxon or elements (species) included in a taxon, de Queiroz and Gauthiers system is less stable than the Linnaean system. Linnaean ranks communicate limited information about inclusivity of taxa, but abandonment of ranks results in the loss of such information. As cladistic hypotheses advance, taxa named under de Queiroz and Gauthiers system can change their level of generality radically, from being part of a group to including it, without any indicative change in its spelling. The Linnaean system has been retained by taxonomists because its hierarchic ranks are logically compatible with nested sets of species, monophyletic groups, and characters. Other authors have offered conventions to increase the cladistic information content of Linnaean names or to replace them with names that convey cladistic knowledge in greater detail; de Queiroz and Gauthier sacrifice the meaning of taxon names and categorical ranks in favor of spelling stability.

Undisciplined thinking: morphology and Hennig’s unfinished revolution

There was a time, not long ago and prior to Hennig (1966), when taxonomy was widely dismissed as a mere service to ‘real’ – read experimental – sciences. Taxonomists were regarded by many to have nothing more to contribute to modern biology than the pragmatic role of identifying species and keeping track of their names. This was a legacy of the conflation of systematics with genetics by Huxley (1940), Mayr (1942) and others (see Wheeler, 1995, 2008a). Hennig re-elevated taxonomy, as phylogenetic systematics, to its rightful place as a rigorous, free-standing and central field of the biological sciences. Taxonomy is typically performed best when it is carried out for its own sake. Taxonomists are motivated to explore species, character diversity and phylogenetic relationships within monophyletic groups. The ultimate goal of taxonomists is a phylogenetic classification with associated scientific names, what Hennig described as biology’s general reference system. Oh yes, they make species identifiable, too. Current molecular initiatives, including DNA barcoding and DNA taxonomy, threaten to reduce species discovery as well as classifications to nothing more than a service. Because ‘new’ species would be ‘discovered’ on the basis of phenetic distances only, DNA barcoding might be described better as a disservice to biology (Prendini, 2005; Wheeler, 2005). After all, it offers only arbitrary averages, by contrast with explicitly testable alternatives, such as the phylogenetic species concept (Wheeler & Platnick, 2000). DNA taxonomy (in the sense of Tautz et al., 2003) is another flawed approach that would diminish the information content of classifications (e.g. Lipscomb et al., 2003). The trend in molecular phylogenetics (‘phylogenetic biology’) has been to increasingly marginalize the evidential basis of taxonomy and to treat the creation of ‘trees’ largely as a service to those same ‘real’ sciences. It is not coincidental that central to taxonomy ‘done for its own sake’ is a detailed study of characters, whereas most molecular phylogenies are published without characters. Morphology is regarded increasingly as an optional adjunct to molecular phylogeny, rather than an essential component of our understanding of species and their diversification. It is said that morphology provides few characters by comparison with molecular sources, and that its complex characters are inconveniently difficult to interpret and unacceptably subjective in their analysis. As a result, we are educating few young comparative morphologists and homogenizing ‘phylogenetic biology’ to be effectively little more than molecular ‘trees’ and morphology little more than literature reviews. The number of projects in which serious original morphological study is undertaken is alarmingly few, meaning that existing morphological hypotheses are untested, mistaken homology assessments are perpetuated and new morphological characters are undiscovered. The tragic loss represented by this neglect of comparative morphology has yet to be felt. Molecular phylogenies have concerned themselves largely with the reinterpretation of known taxa, and especially those bearing controversial ‘key’ morphological achievements, such as the evolution of flight in insects, vascular tissues in plants and, of course, the great tritomy of human, chimp and gorilla. Increasingly, it seems that molecular phylogenies are performed in service to others, to provide chronological patterns to biologists studying some attribute of organisms of sufficient complexity to be of inherent interest. The same putative virtue of simplicity that is claimed to make the interpretation of phylogeny from molecules less subjective deprives amino acids of sufficient complexity to store historical information. That only emerges from the next step in complexity: the sequence of amino acids in strands of DNA. Just as this minimal complexity adds some imperfect historical information, increasingly complex characters – genes, functionally linked genes, proteins, folding patterns, tissues, cells, ontogenetic pathways and morphology – each in turn potentially stores more and more historical information. This information is more difficult to interpret. Nevertheless, as has been well established, it can be made fully explicit and testable (Hennig, 1966; Farris, 1979; Gaffney, 1979; Nelson & Platnick, 1981; Wiley, 1981; Schuh, 2000). It takes time to begin to interpret the techniques used by Leonardo da Vinci to capture the mystique of Genevre D’Benci, and considerably Correspondence: Quentin D. Wheeler, College of Liberal Arts and Sciences, Arizona State University, PO Box 876505, Tempe, AZ 85287-6505, U.S.A. E-mail: quentin.wheeler@asu.edu

Does counting species count as taxonomy? On misrepresenting systematics, yet again

Recent commentary by Costello and collaborators on the current state of the global taxonomic enterprise attempts to demonstrate that taxonomy is not in decline as feared by taxonomists, but rather is increasing by virtue of the rate at which new species are formally named. Having supported their views with data that clearly indicate as much, Costello et al. make recommendations to increase the rate of new species descriptions even more. However, their views appear to rely on the perception of species as static and numerically if not historically equivalent entities whose value lie in their roles as “metrics”. As such, their one‐dimensional portrayal of the discipline, as concerned solely with the creation of new species names, fails to take into account both the conceptual and epistemological foundations of systematics. We refute the end‐user view that taxonomy is on the rise simply because more new species are being described compared with earlier decades, and that, by implication, taxonomic practice is a formality whose pace can be streamlined without considerable resources, intellectual or otherwise. Rather, we defend the opposite viewpoint that professional taxonomy is in decline relative to the immediacy of the extinction crisis, and that this decline threatens not just the empirical science of phylogenetic systematics, but also the foundations of comparative biology on which other fields rely. The allocation of space in top‐ranked journals to propagate views such as those of Costello et al. lends superficial credence to the unsupportive mindset of many of those in charge of the institutional fate of taxonomy. We emphasize that taxonomy and the description of new species are dependent upon, and only make sense in light of, empirically based classifications that reflect evolutionary history; homology assessments are at the centre of these endeavours, such that the biological sciences cannot afford to have professional taxonomists sacrifice the comparative and historical depth of their hypotheses in order to accelerate new species descriptions.