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Beyond CladisticsThe Branching of a Paradigm$

David M. Williams and Sandra Knapp

Print publication date: 2010

Print ISBN-13: 9780520267725

Published to California Scholarship Online: March 2012

DOI: 10.1525/california/9780520267725.001.0001

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Floras to Phylogenies: Why Descriptive Taxonomy Matters

Floras to Phylogenies: Why Descriptive Taxonomy Matters

Chapter:
(p.76) (p.77) Five Floras to Phylogenies: Why Descriptive Taxonomy Matters
Source:
Beyond Cladistics
Author(s):

Sandra Knapp

J. Robert Press

Publisher:
University of California Press
DOI:10.1525/california/9780520267725.003.0005

Abstract and Keywords

Taxonomy has also been characterized as description, phylogeny, and identification. Description is central to most visions of what the science of taxonomy should be, but the importance and prominence of descriptive taxonomy as an enterprise has been in sharp decline, particularly relative to the advances made in phylogenetics with the adoption of molecular techniques. In the context of the future of cladistics, descriptive taxonomy takes on a new importance and relevance as the evidence on which reciprocal illumination is based. This chapter discusses some of the reasons why descriptive taxonomy is critically important for both the generation and evaluation of further data on the biology of organisms. It uses the term “description” to mean a synthetic word picture of an organism, encompassing morphological characteristics drawn from specimens, both living and preserved. It draws ideas from the botanical tradition of floristics and monography, although the description as an essential building block for future hypothesis development is applicable in many groups of organisms.

Keywords:   descriptive taxonomy, description, phylogeny, cladistics, reciprocal illumination, biology, floristics, monography

The centrality of taxonomy (or systematics; we will here use these two terms as synonymous) to the study of diversity is often taken for granted, but the decline in the discipline decline has been highlighted through various reports (House of Lords 1992, 2002, 2008) and funding initiatives (such as the U.S. National Science Foundation’s Partnerships for Enhancing Expertise in Taxonomy [PEET]—see Rodman and Cody 2003; and the Planetary Biodiversity Inventory Program [PBI]—see Wheeler 2004, Page 2008; the UK’s BBSRC Co-Syst program—see http://wwwlinnean. org/co-syst). The field of taxonomy appears to be entering a time of unprecedented change and perhaps renovation (Godfray and Knapp 2004), but what needs change, how that change can be affected, and just what sort of taxonomy we might need for the future are still under discussion (e.g., European Distributed Institute of Taxonomy [EDIT] 2007).

If the field of taxonomy can be characterized as interlocking spheres of endeavor, we can divide it in many different ways—a report charting the science assembled by the community in the mid-1990s (see Anonymous 1991) suggested that the tasks of “systematics” could be seen as three central “missions”: (1) “survey, discover, inventory and describe global species diversity accurately, efficiently, and rapidly; (2) analyze (p.78) and synthesize the information derived from this global discovery effort into a predictive classification system that refects the history of life; and (3) organize the information derived from this global program in an ef-ficiently retrievable form that best meets the needs of science and society (Systematics Agenda 2000). Put more simply, Systematics Agenda 2000 laid out a set of priorities where species were catalogued, the tree of life was constructed, and the resulting information was made accessible in many ways. Taxonomy has also been characterized as description, phy-logeny, and identification (Knapp 2008a). Description is central to most visions of what the science of taxonomy should be, but the importance and prominence of descriptive taxonomy as an enterprise has been in sharp decline, particularly relative to the advances made in phylogenetics with the adoption of molecular techniques (Wheeler 2004, 2008).

Moreover, most current summaries of what taxonomy needs to best enter into the twenty-first century are largely limited to synopsis or inventory—the naming and listing of species of organisms. Logically extended, this definition of descriptive taxonomy suggests that the role of description is to give names to the terminals in a cladogram or tree, and principally to allow communication about the entities we designate as worth naming in nature. In this conception, description is the same as naming and listing. This view owes much to the erroneous characterization of the discipline as “essentialist” and “typological” (Winsor 2006); which has contributed to the narrowing of our appreciation of what taxonomy can contribute to the rest of biology. Much discussion and effort have recently been put into the provision of names lists (see Godfray 2002; EDIT 2007; papers in Wheeler 2008) for use in assessment and monitoring. Global databases such as the Global Biodiversity Information Facility (GBIF, www.gbif.org), Integrated Taxonomic Information System (ITIS, www.itis.gov), and Catalogue of Life (www.catalogueoflife.org) all provide names lists with minimal descriptive information. Names lists, especially rigorously synonymized ones, are of course essential for counting exercises and for establishing the scale of the numerical diversity of life on Earth. Less discussion has centered on the importance of the provision of comparable descriptive information about species and its future utility for organismal science, although some taxon based databases are working toward this goal (see Creating a Taxonomic E-Science [CATE], www.cate-project.org; Solanaceae Source, www.solanaceaesource.org). The recently established Encyclopedia of Life (www.eol.org) where names lists will be reinforced by the addition of a wide variety of content is a step toward the provision oage (p.79) more descriptive information online, but much of the discussion as to what constitutes “descriptive taxonomy” still centers on the provision, on paper or electronically, of names and lists.

We would contend that description is more than naming; descriptive taxonomy needs to be seen as more than the “mere” naming of species. A good taxonomic description is just that, a description of the organism— what it looks like, where it lives, sometimes even the base sequence of portions of its DNA. The characters used in both phylogeny and iden-tification are part of a description and are every bit as important as the name itself. In fact, the name is really just a shorthand way of accessing the information contained in the description itself, just as a person’s name is easier to use than repeating a physical description each time one wants to refer to an individual. Description can be thought of as the Cinderella of taxonomy because it is largely invisible but critical to the functioning of both phylogenetics and identification—thought by some to be more obviously practical, the other components of the taxonomic whole (Knapp 2008b). Without it, however, the rest would collapse—how can you construct a phylogeny without knowing what you are constructing a phylogeny of, or how can you identify an organism without its having an identity and way to recognize it in the first place?

Any decision as to the specific or other taxonomic status of an organism is an hypothesis (Wheeler 2004; Knapp 2008a, 2008b), subject to test using new data or new interpretation of data. Taxonomic practice in botany involves setting the boundaries for that hypothesis, typically by consulting specimens for a variety of characters (morphological and molecular), then assigning a name by applying the rules as laid down in the International Code of Botanical Nomenclature (McNeill et al. 2006), and finally the preparation of a synthetic description taking into account variation across the set of objects (specimens) hypothesized to be included in the species. Models of how this process works have been developed with the intention of capturing taxon concept circumscription and automating description generation (Pullan et al. 2000, 2005), but the sheer scale of data entry required may make these impractical in the near term (Berendsohn 1995).

In the context of the future of cladistics, descriptive taxonomy takes on a new importance and relevance as the evidence on which reciprocal illumination is based. Hennig’s (1966) concept of reciprocal illumination is often not articulated, but it has become (or should have become!) the background wallpaper against which all hypotheses of relationships, whether based on molecules or morphology, are assessed. Reciprocal (p.80) illumination has been characterized as the reevaluation of characters (= homology assessments; see later discussion) in order to minimize character conflict (Hawkins 2000) and has generally been seen in the context of matrix development or manipulation through such methods as character weighting or transformation series analysis (Siebert 1992; Patterson and Johnson 1997; but see Rudall 2000). Coding of characters has long been of interest to those undertaking analysis using morphological data (Stevens 2000), but it is arguably less problematic when using DNA sequence data in phylogeny reconstruction. Since the advent of widespread use of DNA sequence data in phylogenetic reconstruction, the idea of reciprocal illumination and character reevaluation has become less prominent. This is based on the truism that the character states themselves are unambiguous (the bases are A, G, C, or T—no overlap exists) and that no intermediate states exist (Brower and Schawarach 1996; Brower 2000), but that the characters (i.e., the positions in the alignment) can be problematic to align (i.e., to infer their homology) (Stevens 2000).

Reciprocal illumination, however, is just as applicable with molecular data as with morphological, as alignments, which can be thought of as the characters (Stevens 2000) or homology assessments using sequence data, are subject to error and/or misinterpretation. It is not our purpose here to evaluate the perils and pitfalls of homology assessment or to compare molecular with morphological data (see Wortley and Scotland 2006 for an analysis), but instead to explore some of the reasons descriptive taxonomy is critically important for both the generation and evaluation of further data on the biology of organisms. We here use the term description to mean a synthetic word picture of an organism, encompassing morphological characteristics drawn from specimens, both living and preserved. The body of work from which we draw our ideas is the botanical tradition of floristics and monography, but the description as an essential building block for future hypothesis development is applicable in many groups of organisms.

Floras and Monographs

Plants play a fundamental role in all ecosystems; thus their characterization and identification have long been of interest. Other biologists often need to identify plants in order to describe the habitats in which their particular organisms operate; to facilitate these sorts of tasks, botanists (p.81) have long written descriptive guides to the plants of particular places (Knapp 2008a). What distinguishes such descriptive guides, floras, from mere names lists are keys for identification and descriptions with which to compare specimens. Floristics has a long history in botany, beginning with the herbals (Arber 1912). Linnaeus (1751) in Philosophia Botanica said a flora was “the vegetation growing naturally in one place.” Floris-tics can be distinguished from monography (but see later discussion) by being place, rather than taxon, focused. The flora as identification guide was developed first by Lamarck in his landmark Flore françoise (1779) in which dichotomous keys and French language descriptions were provided for all known French plants, allowing a wide variety of people to learn about plants (Scharf 2009). Later editions (Candolle 1805) were sophisticated developments of explicitly artificial systems aimed at facilitating identification, rather than natural systems aiming to describe relationships (Scharf 2009). Throughout the nineteenth and twentieth centuries, botanists have documented the floras of regions of the globe, often taking many decades (see Knapp 2008b) and causing taxonomic problems when regions treated were small and global views not taken (Knapp et al. 2001). Since floras are usually explicitly about facilitating identification and not about the phylogenetic relationships of plants, they are sometimes seen as less “scientifc” or less rigorous than taxon-based monographs (Grimes 1998). Carefully researched floristic accounts, however, can approach a monograph in scope and quality, and blur the somewhat artificial (if not completely absent!) dividing line between floras and monographs (Maxted 1992). A flora is a multipurpose tool and can be considered the baseline for understanding national, regional, and local plant diversity.

Monographs are traditionally defined as taxonomic (systematic) works presenting global coverage of a particular (monophyletic) plant group. Relationships among the members of the treated group are generally considered a cornerstone of a monograph, and this focus on a “natural” rather than “artifcial” system of classification (see Scharf 2009) has led some (Grimes 1998) to suggest that regional treatments of plant groups are premature before a complete phylogenetic understanding is achieved. Grimes (1998) suggests that monographs more correctly delineate species than do floras and in addition provide a phylogenetic scaffolding on which other hypotheses can be hung. Others (Funk 1993) have argued that floras can be effectively used to construct phylogenetic hypotheses for use in a wide range of disciplines, and that the time necessary to complete in-depth monographic treatments of all plant groups is just not (p.82) available to us in the current situation (Knapp et al. 2001; EDIT 2007). Regardless of whether one feels monography or floristics should take priority (we feel both have an important role to play), both these types of work share a core of descriptions—word pictures of the plants being treated. A monograph is not just a phylogenetic tree or a cladogram, just as a flora is not just a list of the names of the plants growing in a particular region.

The descriptive core of both monographs and floras is composed of a series of parallel descriptions of the summary morphology of each species, with all characters considered measured and provided. Floras usually have shorter, less exhaustive descriptions than do monographic works (compare, e.g., the treatment of Lavandula in Flora Europaea [Guinea 1972] with that in the monograph by Upson and Andrews [2004], or the treatment of Argyranthemum by Press [1994] with that of Humphries [1976]). The creation of parallel descriptions, in which each has all characters, has its roots in the search for the “true” natural classification; in the eighteenth century, Michel Adanson considered the totality of compared descriptions critical for determining the “natural order” (Winsor 2004). This, of course, depends on descriptions being completely comparable. Characters are only of use in either phylogeny or identification if they are compared (Rieppel 2004), thus making the parallel nature of descriptions essential for their subsequent use in any new analysis.

Ultimately it is the objects themselves that possess characters, and if all specimens were accurately databased with all features measured (perhaps a reality in the not so distant future, see Wheeler 2008), then we would be able to generate synthetic descriptions from a set of specimens ad hoc (see Pullan et al. 2005). The online databases, specimen images, and character measurements represent the primary data from floristics and monography, and they are the raw materials for the descriptive element, but they currently do not replace it completely.

Why Descriptive Taxonomy Matters

Hypotheses generated from taxonomy are critical to many other fields in biology (Godfray 2002; Gotelli 2004; Mace 2004). Phylogenetic trees are often taken as the most important product needed for other biologists, but a tree not well rooted in the organisms is alone not really the basis for future exploration of the evolutionary process. Keys are critical (p.83) for identification; Gotelli (2004) cites them as the single most useful taxonomic product for macroecologists, more important even than robust phylogenetic hypotheses. Keys alone, however, often only use a few of the many characters—those useful for identification—and can sometimes serve to confuse or mislead if a more complete word picture (description) of the organism is not provided as a backup (see Alcock 2009). Both keys and phylogenetic trees (via the terminals used and their previous identification) stand on the foundation of a good morphological characterization of taxa; a synthetic description is a check, but as a summary of the variation within a given taxon, it can also be revisited and reevaluated.

Descriptions can be used to generate data sets for cladistic analysis (Funk 1993), but their real value lies in their actual preparation. By preparing a morphological description via examining specimens, a botanist is forced to examine the organism carefully and compare it with relevant taxa previously described. Wortley and Scotland (2006) have shown that morphological character sets are often of equal utility (measured as number of parsimony–informative character–state changes) as much larger molecular data sets, and they suggest that molecular data sets alone are not necessarily the most useful for reconstructing robust trees. A morphological data set, while smaller, can often have more utility than the number of characters might suggest. Choice of characters is important, and morphological data sets are smaller in general due to this choice. Choosing the morphological characters to include is the equivalent of a priori character weighting (see Wägele 2004), and the production of parallel descriptions allows others to test the hypotheses of homology that these characters represent through reciprocal illumination. Homology is the way in which to understand organisms, not just name them, and leads to further hypotheses about relationships, function and process.

Descriptive taxonomy should be seen as the foundation for new ideas and views on how the world works (Winsor 2009). Charles Darwin, at the same time as beginning his species notebooks and articulating his ideas about evolution by natural selection, began an in-depth taxonomic study of barnacles (Darwin 1851, 1854) in order to better understand characters and how they were distributed. His time spent on barnacles (1846–1854) allowed him to see in detail how characters relate to one another (homology), and these data certainly influenced his conception of life as interconnected through branching evolution (Winsor 2009). His descriptions of the whole organism—the phenotype—in the barnacle monographs allowed others to assess his ideas of character identification (p.84) and relationships; this information, including his keys, is still in use today. Descriptive taxonomy is far from being a sterile production of lists of names and species, but it should instead be seen as the crucible in which new ideas about taxa and their relationships are generated using the Hennigian principle of reciprocal illumination.

Acknowledgments

Our ideas in this contribution come from discussions over many years not only with Chris but also with other colleagues at the Natural History Museum, London, and elsewhere. A Planetary Biodiversity Inventory award from the National Science Foundation (DEB-0316614, “Solanum: A Worldwide Treatment”) supports S.K.’s monographic work, and J.R.P. is supported by KeyToNature (eContentplus program of the European Commission, ECP-2006-EDU-41001).

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