AmphibiaWeb Taxonomy
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Contents:
I. AmphibiaWeb Taxonomy (Version 2.0)
AmphibiaWeb introduces its new taxonomy for families (Version 2.0, March 1, 2012). Amphibian taxonomy was relatively stable for decades, as summarized by Frost (1985) and Duellman and Trueb (1986). The advent of direct DNA sequencing methods in the early 1990's enabled tests of previous hypotheses of phylogenetic relationships. In turn, new understandings of phylogeny led to suggestions for taxonomic revision. The first large-scale taxonomic treatment for all of living amphibians (Frost et al. 2006) proposed radical changes and additional publications have made further taxonomic revisions. The taxonomy initially used by AmphibiaWeb (February, 2000) was subsequently modified, but cautiously and with much discussion; we have favored stability over new arrangements that might have proven temporary. The AmphibiaWeb team has decided that there is sufficient general agreement within the community of amphibian phylogeneticists and taxonomists to warrant the adoption of an revised taxonomy. The most salient difference is an increase in the number of families recognized. The specific rationale for these changes is explained below. Taxonomy is a living, vibrant area of science, and we anticipate that ongoing research will require future changes. AmphibiaWeb will continue to make changes thoughtfully in order to best serve our wide and diverse community of users.
II. Perspective on Taxonomy
In 1735, Swedish botanist Carl Linnaeus (1707-1778) introduced the familiar system of classification that is used today, consisting of a two-part name (genus and species) to uniquely identify each species of organism, and hierarchical categories (e.g., family, genus, species) for grouping them. (Linnaeus did not use Kingdom and Phylum.)
Since the publication of Darwin's The Origin of Species in 1859, the classification of species assumed new significance. Systematists began working towards discovering and describing the evolutionary relationships among species in addition to naming and classifying them. In 1950, the late German entomologist Willi Hennig revolutionized the practice of systematics by providing a method for inferring the true branching pattern of evolutionary history (phylogenetic systematics), and argued that classification should reflect only phylogenetic relationships, not overall similarity.
Efforts to explicitly meld phylogenetic relationship with taxonomy have conflicted with the International Code of Zoological Nomenclature, principally relating to the ranking of taxa. Proposals for a phylogenetic taxonomy, in which taxonomic ranks are abandoned (de Queiroz and Gauthier 1990), have been resisted by the community of taxonomists despite the advantages of such a system: tying taxonomy directly to phylogeny enables inferences of evolutionary history to be drawn directly from the classification. AmphibiaWeb will continue to track advances in phylogenetic taxonomy and in the meantime, while using traditional taxonomy, attempt to recognize only monophyletic taxa.
III. Goal of the AmphibiaWeb Taxonomy
The goal of the AmphibiaWeb taxonomy is to provide a stable reference system for ordering the taxonomic accounts on AmphibiaWeb, as well as to serve community databases that wish to incorporate it (i.e., GenBank, IUCN). In this spirit, we will endeavor to (1) solicit feedback from taxonomic experts, (2) document changes in numbered versions, and (3) provide ready access to this taxonomy.
AmphibiaWeb remains open to improving its taxonomy. However, our decisions will be guided by a general goal of relative stability. It will not be possible to integrate incompatible classifications proposed by different authors. In these cases, our taxonomic decisions will be informed by careful consideration of factors discussed below. Some argue that stability is not a goal of taxonomy and that provocative taxonomies stimulate further work. For the purposes of AmphibiaWeb, our position is that the practical benefits of stability for the larger community should be accorded more weight. The AmphibiaWeb taxonomy takes into account taxonomic treatments by Dubois (2005), Faivovich et al. (2005), Frost et al. (2006), Pyron and Wiens (2011), and Blackburn and Wake (2011), as well as much additional literature. The current AmphibiaWeb taxonomy is unique and it is based on critical evaluations of publications (see Literature Cited) and the general aim of relative taxonomic stability.
IV. Stability
We consider taxonomic stability to be a worthwhile goal. To achieve this goal, we depend not on the influence of authority, but on progress in phylogenetic analysis, which is producing increasingly well-supported hypotheses of relationships. As clades become well supported through repeated verification, names applied to those clades will stabilize. It is possible that parts of the tree may never become well supported. For instance, Ranidae is a large clade with multiple smaller clades; however, relationships among the smaller clades are not well supported. Thus, we could recognize one very large family made up of many smaller clades treated as subfamilies (i.e., Ranidae sensu lato with, e.g., Raninae, Rhacophorinae, Mantellinae, Arthroleptinae, etc.), or instead recognize each of the smaller clades as families (e.g., Ranidae, Rhacophoridae, Mantellidae, Arthroleptidae). These are equally acceptable; we choose the latter option in part because the single combined family would be very large, but also because leading taxonomic researchers are increasingly using the multiple-family option.
Often when phylogenetic relationships within a large taxon are resolved, the taxon is split into smaller taxa and once-familiar names change in ways that can be confusing. When changes were proposed for the large genus Rana, the familiar species Rana catesbeiana became Lithobates catesbeianus. The general point is that names that have been used for many decades become separated from an often very large scientific and popular literature. It is not the informed taxonomist who will be confused, but rather other researchers, educators, conservationists, or members of the public who use taxonomy as an information source and reference.
We favor taxonomic stability in most instances where change in the name of a taxon is not required, for example, because of non-monophyly. This provides maximal stability for end-users whose mission relies on such lists (e.g., GenBank, IUCN). However, in this version (AmphibiaWeb 2.0) we have not implemented this uniformly, because debate about this issue is still in progress.
Newly introduced genus-species combinations often have been accepted by many non-systematists, under the assumption that the latest publication is necessarily the standard. Nothing in the International Code of Zoological nomenclature requires that the most recent classification be adopted. In fact, the First Principle of the Code states:
"(1) The Code refrains from infringing upon taxonomic judgment, which must not be made subject to regulation or restraint."Thus, a newly published taxonomy should not be interpreted as a formal, mandatory change; it is simply an alternative that should be evaluated alongside other such proposals. While many users will find this frustrating, but it is through this juxtaposition of classifications that synthesis and stability will emerge over time.
V. Criteria for Taxonomic Recommendations
Several criteria are considered in compiling this classification, and we present them here to provide a context for our taxonomic decisions. Taxonomy is a sophisticated part of science, and there is no universally accepted procedure for applying these (and even more) criteria.
1. Monophyly. This is of primary importance, and is well accepted for all supraspecific taxa.
2. Stability. This is the continued association of names with stable content. Ranked names with commonly accepted content should not be applied to other taxa with substantially different content. The Turtle Taxonomy Working Group (2009), for example, has strongly recommended this practice.
3. Expertise of authors. We favor taxonomies by authors who have demonstrated systematic expertise with a particular taxon, through publications, especially at the rank for which changes are proposed.
4. Usefulness, or general "acceptance" by the amphibian community. Usefulness is an important criterion but in general, its meaning has not been carefully considered. A taxonomy that adds phylogenetic information is useful. However, an increase in phylogenetic information but with unnecessary changes in name stability may not be as useful. An increase in phylogenetic resolution and change in taxonomy, especially rank, are often treated as necessarily connected, but the two are distinct.
Specialists may find new names useful, whereas others may see negative implications (for example, changing the name of a federally protected species whose name is embedded in legal statutes). Continuing disagreement about the names for model organisms highlights this issue (for flies, Drosophila vs. Sophophora; for frogs, Xenopus vs. Silurana).
5. Ranked taxa. Most biologists consider ranks to have little biological significance, although they are widely used by paleontologists. In our view, ranks promote "list-thinking" over "tree-thinking", and it is the latter that dominates the thinking of most practicing systematists today.
6. Degree of divergence. There is some value in considering depth of divergence with respect to time since separation from sister taxa, extent of phenotypic divergence, and degree of genetic divergence (e.g., molecular traits). However, this approach can be carried too far, as when a monophyletic taxon is pulled out of a more inclusive clade, thereby rendering the residue a paraphyletic taxon (birds treated as a class, while at the same time the remaining reptiles are treated as a paraphyletic class). We favor evaluating divergence in a way that balances long-term usage with the primary consideration of monophyly.
7. Degree of Support. Judging whether a clade is well supported (e.g., bootstrap support or posterior probabilities), the relative extent of sampling, and the amount and kinds of data supporting clades are important elements in taxonomic judgement. Furthermore, the quality of data and the extent of taxonomic sampling in these analyses are also part of such considerations.
VI. Other Considerations
1. There are rational alternatives to the splitting of taxa at the level of genus. Different taxonomists are exploring the use of subgenera, which enables recognition of subordinate clades while maintaining stability.
2. The rank of family is far less important for most purposes than the genus and species names. As in the case of genera and subgenera, there are appropriate ranks that would enable the expression of phylogenetic information. For example, advocates of the unranked taxon Terrarana (which we do not recognize because it is outside the Linnaean hierarchy and not under the authority of the International Code of Zoological Nomenclature) as a phylogenetic "umbrella" for five families (four only recently established) could have accomplished the same goal by recognizing a single family with five subfamilies for the biologically very similar members. A consideration in this case is that the total number of species is very large. Somewhat reluctantly we have decided to follow most instances of family splitting because these changes are meeting the approval of working taxonomists and family designations are usually not very important to non-specialists.
VII. Taxonomic Subcommittee
This statement was authored by the taxonomic subcommittee of AmphibiaWeb (David C. Blackburn, California Academy of Sciences; David C. Cannatella, University of Texas, Austin; and David B. Wake, University of California, Berkeley). The AmphibiaWeb taxonomy will undergo changes from time to time as we continue to monitor and evaluate the technical literature.
VIII. Literature Cited
Blackburn DC, Wake DB. 2011 Class Amphibia Gray, 1825. In: Zhang Z.-Q (ed) Animal biodiversity: an outline of higher-level classification and survey of taxonomic richness. Zootaxa 3148: 38-54.
de Queiroz K, Gauthier J. 1990 Phylogeny as a central principle in taxonomy - phylogenetic definitions of taxon names. Syst Zool 39: 307-322.
Dubois A. 2005 Amphibia Mundi. 1.1. An ergotaxonomy of recent amphibians. Alytes 23: 1-24.
Duellman WE, Trueb L. 1986 Biology of Amphibians. McGraw-Hill, New York, 670 pp.
Faivovitch J, Haddad CFB, Garcia PCA, Frost DR, Campbell JA, Wheeler WC. 2005 Systematic review of the frog family Hylidae, with special reference to Hylinae: phylogenetic analysis and taxonomic revision. Bull Amer Mus Nat Hist 294: 1-240.
Frost DR (ed). 1985 Amphibian Species of the World. A Taxonomic and Geographical Reference. Allen Press and Association of Systematics Collections, Lawrence, Kansas, 732 pp.
Frost DR, Grant T, Faivovich J, Bain RH, Haas A, Haddad CFB, De Sa RA, Channing A,Wilkinson M, Donnellan SC, Raxworthy CJ, Campbell JA, Blotto BL, Moler P, Drewes RC, Nussbaum RA, Lynch JD, Green DM, Wheeler WC. 2006 The Amphibian Tree of Life. Bull Amer Mus Nat Hist 297: 1-370.
Pyron A, Wiens JJ. 2011 A large-scale phylogeny of Amphibia with over 2,800 species, and a revised classification of extant frogs, salamanders, and caecilians. Mol Phy Evol 61: 543-583.
Turtle Taxonomy Working Group [Bickham JW, Parham JF, Philippen HD, Rhodin AGJ, Shaffer HB, Spinks PQ, van Dijk PP]. 2007 Turtle taxonomy: methodology, recommendations, and guidelines. In: Shaffer HB, FitzSimmons NN, Georges A, Rhodin AGJ (eds) Defining turtle diversity: Proceedings of a workshop on genetics, ethics, and taxonomy of freshwater turtles and tortoises. Chelonian Research Monographs, 4. Lunenburg (MA): Chelonian Research Foundation. p. 73-84.