© 2006 Society of Systematic Biologists
Stability and Universality in the Application of Taxon Names in Phylogenetic Nomenclature
Edited by Michael Lee: Associate Editor
1 School of Life Sciences, Department of Biology, Södertörn University College SE-141 89 Huddinge, Sweden E-mail: yann.bertrand{at}sh.se (Y.B.) and mikael.harlin{at}sh.se (M.H.)
2 Muséum National d'Histoire Naturelle, Département Systématique et Évolution CNRS UMR 7138, ‘Systématique, Adaptation, Évolution’, 57 rue Cuvier, 75231 Paris Cedex 05, France
Received December 15, 2005; Revised March 9, 2006; Accepted May 15, 2006 A major task for biological nomenclature and taxonomy is to provide names and tools for communication about biodiversity. This is even more important in times of bioinformatics where scientists often search GenBank and other databases for phylogenetic information. Comparative studies on a large number of unrelated taxa by scientists that are not taxonomic specialists are likely to become even more common in the future. Hence, a nomenclatural system that helps scientists to unequivocally find information about a particular taxon has high priority.
One step towards achieving such a system is the phylogenetic system of nomenclature (PSN) initially developed by de Queiroz and Gauthier (1990, 1992). The PSN differs from traditional rank-based nomenclature (RSN) in that it avoids the connection of a name to a particular taxonomic rank and type. And perhaps more importantly, PSN utilizes more than one reference point (i.e., specifiers) for each name. A major advantage with two specifiers (instead of one type) is that given the specifiers and a phylogenetic tree (including the specifiers), it is rather straightforward to find out the extension of the taxon in question. This is much more difficult within a RSN because the extension of a taxon name is not spelled out in a formal definition. Thus, the PSN seems ideal to provide taxonomic information to users in an explicit and unequivocal way. This is indeed an important task for nomenclature and taxonomy in the future.
Nevertheless, the merits of PSN, as compared to RSN, are still controversial and much debated in systematics. Much of this debate concerns what is meant by a name and the importance of taxonomic stability. Although proponents of RSN often highlights the importance of taxonomic content, proponents of PSN instead highlights the importance of common ancestry (Bryant and Cantino, 2002). Taxonomic stability, also referred to as stability in content (Lee, 1996) and circumscriptional stability (Moore, 1998), corresponds to the stability in the extension of names and is measured in terms of all taxa included in a group referred to by a name; taxa missing in each application of a name compromises this stability (Nixon and Carpenter, 2000).
Related to the issue of stability is the importance for a taxonomic name to be applicable in a wide range of biological contexts, i.e., to have high universality. In phylogenetic nomenclature high universality for a phylogenetic name (hereafter referred to as phylonames) should mean that it could be used in a wide range of phylogenetic analyses and trees. And, as a corollary, high universality of a name also implies that all biologists should use the same name for the same taxon (de Queiroz, 1997; see also Härlin, 2003, 2005).
Although initially agnostic on the issue on taxon content, proponents of PSN have lately come up with methods to stabilize taxonomic content when the choice of phylogenetic hypotheses shift. One such method is to increase the number of specifiers used in a taxon name definition. In the present paper we argue that there is a trade-off between stability and universality in terms of number of specifiers. That is, the current trend in PSN to emphasize stability in content by increasing the number of specifiers in phylogenetic definitions is actually limiting the communication efficiency of phylonames. Thus, even if this practice may increase taxon content stability, it tends to compromise the universality in the application of these names. And the effect may be that we lose the advantage gained by introducing PSN as a replacement for RSN in the first place.
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Taxonomic Stability and The Inflation of Specifiers |
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The defenders of RSN (e.g., Moore, 1998; Benton, 2000; Nixon and Carpenter, 2000; Dyke, 2002; Carpenter, 2003; Kojima, 2003; Moore, 2003; Nixon et al., 2003) argue that a rank-based system is more stable because in the absence of definitional rigidity, taxonomists are free to amend the content of a taxon in order to preserve its original meaning (i.e., content). The following hypothetical example (Fig. 1) may serve as an illustration of this point. In the first phylogenetic context, the clade ((AB)C) is named Aina according to the PSN by using a node-based definition with A and C as specifiers (Aina is defined as the clade stemming from the most recent ancestor of A and C), whereas ((AB)C) is named Aus in the RSN and is provided with the following implicit definition (de Queiroz, 1997): "Aus is defined as the taxon including the species A that is assigned to the category genus." Within the second phylogenetic context, C is hypothesized as sister taxon to A. In the PSN, changes in the phylogenetic hypothesis have a bearing on the association between taxon names and taxon membership. These modifications in evolutionary relationships are managed by an automatic application of the definition to a new phylogenetic hypothesis; in the latter hypothesis Aina includes only A and C. On the other hand, in this situation a "good" rank-based taxonomist would be able to maintain a group with the original intent and keep A, B, and C members of Aus; see Nixon and Carpenter (2000) for the development of this argument in the example of the paleoherbs.
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Whether this is a strength or not of the RSN can certainly be debated. For instance, within the same phylogenetic hypothesis different workers can interpret the same taxon in different ways (splitting and lumping). But, it is worth pointing out that whereas phylogenetic nomenclature relies on explicit definitions of taxon names in the identification of taxon boundaries, the RSN is much more vague and is based on subjective reference to taxon content in order to find taxon boundaries. Within a RSN morphological (or character) similarity in general is often used as additional help to judge whether a taxon belongs or not in a more inclusive taxon (Härlin, 1998a). In any case, taxon content is often considered the major focus in RSN, whereas it hitherto has played only a marginal role in PSN.
But, as mentioned in the introductory section, PSN has moved towards emphasizing also taxonomic stability. And in the latest version of the PhyloCode, there are three different mechanisms to promote content stability: crown-clades, qualifying clauses, and the inflation of specifiers. The crown-clade convention aims to associate well-known names with clades within which both of the basal branches have extant representatives (PhyloCode 2b; Cantino and de Queiroz, 2003). Two types of definition have been added to the PhyloCode specifically to name crown-clades. These are the stem-modified node-based (Wyss and Meng, 1996) and the apomorphy-modified node-based definitions (PhyloCode).
Qualifying clauses (PhyloCode, Article 11.9) represent modifications of the original wordings (i.e., de Queiroz and Gauthier 1990, 1992, 1994) of phylogenetic definitions because they specify, in the definition, phylogenetic conditions under which phylonames cannot be applied (Schander and Thollesson, 1995; Bryant, 1997; Cantino et al., 1997). This practice aims to discard uses of names regarded as too remote from their original intent.
De Queiroz and Gauthier (1990) suggested three types of phylogenetic definition: node-, stem-, and apomorphy-based definitions. All of these types require the use of at least two specifiers. In node- and stem-based definitions, specifiers are specimens or species, whereas apomorphy-based definitions are coined with one character and one taxon (species or specimen) as specifiers.
Numerous contributions to phylogenetic nomenclature (Schander and Thollesson, 1995; Cantino et al., 1997; Sereno, 1999, 2005; Bryant and Cantino, 2002; Joyce et al., 2004) suggest that one way to increase taxonomic stability is to use multiple specifiers in phylogenetic definitions. This practice is based on the assumption that the more specifiers that are included in a definition, the more stable in terms of taxon content the reference of the name tends to be, i.e., the name will necessarily refer to all its specifiers. Consequently, the draft of the PhyloCode contains two recommendations demonstrating the shift in focus toward content stability in the wording of node- and stem-based definitions. First, Recommendation 11D promote this kind of stability in node-based definitions and states that "In a node based definition, it is best to use a set of internal specifiers that includes representatives of all subclades that credible evidence suggests may be basal within the clade being named ..." From this follows that "Constructing a node-based definition in this way will reduce the chances that, under a new phylogenetic hypothesis, the name will refer to a less inclusive clade than originally intended." (PhyloCode). Second, Recommendation 11E is the equivalent for stem-based definitions: wherein "... it is best to use a set of external specifiers that includes representatives of all clades that credible evidence suggests may be sister group of the clade being named." The reason is that "[c]onstructing a stem-based definition in this way will reduce the chance that under, a new phylogenetic hypothesis, the name will refer to a more inclusive clade than originally intended."
In line with these recommendations, most names presented at the first meeting (held in Paris) of the International Society for Phylogenetic Nomenclature (Laurin and Cantino, 2004) were defined with a large number of specifiers in order to attain higher taxonomic stability (see the meeting abstracts available at http://www.ohiou.edu/phylocode/IPNM.pdf). Arguably, some form of stability in content is a desirable property for most nomenclatural systems, but stability should not conflict with more fundamental aims (Härlin, 2003, 2005). The main thesis we shall develop in the following sections is that the practice of using more than the two mandatory specifiers for node- and stem-based definitions hampers the requirement for clarity and universality as defined above.
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The Quest for Taxonomic (Content) Stability and Its Consequences |
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TopTaxonomic Stability and The...The Quest for Taxonomic...Choice of SpecifiersPhylogenetic FreedomConcluding RemarksAcknowledgmentsReferences |
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Below we show how some of the phylonames proposed at the Paris meeting would perform in practice from the standpoint of clarity and universality. We have selected phylonames coined by Cantino and Olmstead for Lamiaceae and clades included within (Table 1). The reason is that these names have previously been discussed from the perspective of taxonomic stability in the literature on phylogenetic nomenclature (Cantino et al., 1997, 1999). We have also studied the name Lamiales(and clades included within) as defined by Olmstead and Cantino in Paris. Due to the recent disintegration of Scrophulariaceae sensu stricto, these names constitute a case study on how the PSN behaves in a context of major perturbations in phylogenetic hypotheses. Finally, we have included phylonames of Foraminifera and of clades found within (Table 2) for two reasons: they peak in the number of specifiers (15 for the phyloname Foraminifera) and the definitions contain both extant and extinct species.
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We reviewed the literature for phylogenetic trees in which the selected phylonames potentially could be applied. We were especially attentive to studies using the same rank-based names as the converted names proposed during the Paris meeting. It may be argued that we do not give a fair picture of the PhyloCode's full potential because all the phylogenies under scrutiny were constructed before the phylonames. However, we nevertheless believe that we provide a realistic estimation of the difficulties that the PSN will encounter in practice once implemented. Our examples (e.g., Table 1, Table 2, Table 3) provide ample evidence for this.
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With this in mind, we reviewed 45 articles containing phylogenetic hypotheses for the selected groups. In all these studies, we found 97 putative phylonames, e.g., in a phylogeny of the family Lamiaceae we considered hypotheses where the phyloname Lamiaceae potentially could be applied (Table 3). However, of these 97 phylonames we concluded that only 6 could be applied unambiguously. The reference of the other 91 names could not be unequivocally determined. This discrepancy is due to four factors: the lack of inclusion of original specifiers, the uncertainty of specifiers' positions, the presence of molecular trees without any morphological character optimizations, and the use of both extant and extinct specifiers in definitions. These observations seem to contradict one of the main goals of PSN, i.e., to decrease ambiguity in taxon name reference as compared to RSN.
The absence of specifiers in the studies at hand is the most frequent problem. For instance the phyloname Verbenaceae, presented in Paris, has been erected as a node-based definition by Olmstead and Cantino with the species Verbena officinalis, Duranta erecta, Citharexylum ligustrinum, and Petrea volubilis as specifiers. In their phylogenetic hypothesis of Labiatae and Verbenaceae inferred from rbcL sequences, Wagstaff and Olmstead (1997) included 61 species in their data matrix. However, Duranta erecta and Citharexylum ligustrinum are missing from the sample and we are unable to determine explicitly where these two species branch in the phylogenetic tree. Therefore, the phyloname Verbenaceae cannot be applied in this study. Although a sequence from a member of the genus Verbena was included (Verbena bonariensis), another species of the genus Verbena was used as specifier (V. officinalis), which means a potential reference problem of the name Verbenaceae. It is arguable that the phylogenetic position of V. bonariensis may yield evidence on the position of V. officinalis, but using genus information as surrogate for phylogenetic information goes against the desire of independence of the PhyloCode from Linnaean ranks above species level (see de Queiroz, 1997) and also against the clarity requirement for any valuable system of nomenclature. This is even more of a problem in large-scale phylogenies that mention genera (e.g., Cantino, 1992) or families (e.g., An-Ming, 1990) as terminal taxa. Surrogate methods have been shown to be problematic in other areas (Bertrand et al., in press) and should be avoided also in purely taxonomic methods. Supertree techniques (Wilkinson et al., 2005) could be one way to circumvent these problems. Given sufficient taxon overlap between hypotheses, it will be possible to construct a supertree with all specifiers of a phyloname. But to facilitate retrieving relevant input trees in the first place, ideally each included tree (in the supertree) should contain all (or at least as many as possible) of the specifiers to keep up with the explicitness introduced by PSN. In any case, one way or the other all specifiers in a phylogenetic definition need to be considered to find out the extension of a phyloname.
Kaufmann and Wink's (1994) work on the molecular systematics of the Nepetoideae illustrates the problem for apomorphy-based definitions raised by molecular trees that do not contain optimizations of morphological characters. At the Paris meeting, Cantino and Olmstead presented an apomophy-based definition for Nepetoideae using hexacolpate pollen and Nepeta cataria as specifiers. Although Kaufmann and Winks have included N. cataria, the absence of morphological character optimization renders the phyloname Nepetoideae inapplicable in their phylogenetic hypothesis unless additional information is presented. To minimize vagueness and enhance explicitness (morphological), characters used as specifiers must be optimized on the tree under consideration. This can readily be done also on trees based on molecular data and is common practice in cladistics.
Nothing in the PhyloCode prevents the use of molecular characters as specifiers, but all apomophy-based definitions proposed to date, to the best of our knowledge, are based on morphological features. Molecular data in relation to apomorphy-based definitions are controversial mainly due to alignment issues. Lee (1998) suggests that this type of definition should be restricted to morphological studies. However, such a recommendation runs against the universality principle because names defined with apomorphy-based definitions are applicable only in trees with the morphological character optimization in question. Moreover, it highlights a divorce between molecular and morphological phylogenetics, whereas several studies are demonstrating that the two types of characters are in some cases neither quantitatively nor qualitatively different (Hillis and Wiens, 2000).
Finally, the use of both extant and extinct specifiers in definitions is also related to the problem of character choice in phylogenetic studies. This issue is brought to the fore by the definition of Soritacea (a group of foraminiferans) established by Richardson at the Paris meeting. Richardson based her definition on a phylogenetic study that contained both extinct and extant taxa of Soritaceae (Richardson, 2001). The name Soritacea is defined with a node-based definition using twelve specifiers (both fossil and extant specifiers are used; see Table 2). Richardson also proposes a short version of the definition (Soritacea is defined as the clade stemming from the most recent ancestor of Peneroplis planatus and Marginopora vertebralis). But the sentence "[a] phylogenetic definition of Foraminifera, ..., must reflect both the neontological and paleontological utility of the group ..." suggests that Richardson sees the long definition (including all 12 specifiers both extant and fossil) to be the "correct" definition of the name Soritacea. After reviewing the literature (11 articles; see Table 3) on Foraminiferan phylogenetics, we were unable to apply the name Foraminifera in any phylogenetic tree (because no tree included all specifiers), whereas Soritacea applies only in one study by Richardson (2001).
Having specifiers from both extinct and extant types in a phylogenetic definition is not a theoretical problem per se, but it raises practical difficulties. For instance, in foraminiferan phylogenetics all the trees are based on either pure molecular or pure morphological data and fossils can usually be placed only in morphology-based trees, leaving molecular-based hypotheses out of consideration. The problem is a result of the compartmentalization of biological disciplines; i.e., palaeontology and neontology rarely meet. Large trees constructed from total evidence methods, mixing both type of data, or phylogenies built with supertree techniques are simply rare.
High universality implies that phylonames are applicable in a wide range of phylogenetic trees. The current trend to inflate the number of specifiers also radically decreases the universality of the PSN to the point that phylonames can be readily applied only in their original reference trees (e.g., in the case of Wallander and Albert, 2000).
Highlighting taxonomic stability results in the borderline between a RSN and a PSN to become more diffuse. The importance of stability in content might be a concession to attract users otherwise satisfied by the content-oriented rank-based system. But a phylogenetic system of nomenclature should be a trade-off between the current practices in phylogenetics using a limited number of taxa (mainly due to technical reasons) and the goal of stability. In a distant future, total universality might be achieved with a tree of life including all known extinct and extant species. On the other hand, maximum taxonomic stability corresponds to definitions including as specifiers all members of a given clade and excluding members of closely related outgroups. Hence, the utility of phylogenetic nomenclature as a means for communication across phylogenetic studies decreases. Arguably, such a system would be potentially as useful and meaningful as the map in Lewis Carroll's Sylvie and Bruno Concluded.
"We very soon got six yards to the mile. Then we tried a hundred yards to the mile. And then came the grandest idea of all¡ We actually made a map of the country, on the scale of a mile to the mile¡" "Have you used it much?" I enquired."It has never been spread out, yet," said Mein Herr: "the farmers objected: they said it would cover the whole country, and shut out the sunlight¡ So now we use the country itself, as its own map, and I assure you it does nearly as well." (Carroll, 1893:169).
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Choice of Specifiers |
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Issues pertaining to the choice of specifiers have mainly been tackled from the standpoint of their positions in a tree. In order to buffer taxon content against phylogenetic changes in the position of specifiers, the PhyloCode recommends selecting many basal taxa as specifiers in node-based definitions and many external taxa to the clade being named in stem-based definitions. Moreover, Lee (2005) has addressed the choice of specifiers from the point of view of terminal taxon stability in phylogenetic trees (see also Wilkinson [2006]). He suggests that "wildcard" taxa should be avoided in definitions and that propensity for taxa to change position in successive hypothesis should be quantified with measures of "leaf" stability (Thorley and Wilkinson, 1999).
Without calling the previous recommendations into question, we claim that there is more involved in the choice of specifiers than mere considerations of strength of phylogenetic hypotheses (Härlin, 2005). Some features of taxa that relate to their nomenclatural histories in rank-based systems are already incorporated in the PhyloCode. For instance, Article 11.8 states, "... it would be desirable for a clade whose name is converted from a genus name under a pre-existing code, or is derived from the stem of a genus name, to include the type of the genus name." The reason is the "... interest of consistency with pre-existing codes ...," whereas complete freedom from this constraint is granted for the choice of specifiers that do not form the stem of a phyloname. Therefore, only a study of published phylonames can provide us with an idea on how reference taxa are selected in practice.
We analyzed the 27 phylonames proposed by Cantino and Olmstead for the clades Lamiales and Lamiaceae. In total, they used 78 specifiers for all these names. The authors coined all their names using genera as stems, that is, even the newly erected names and not just the converted names are based on the Linnaean types corresponding to the stem names. For instance, Lamiina possess the standard ending indicating that it is a new name (following Kron's [1997] convention of the ending–ina for phylonames), and is based on the stem Lami-, corresponding to the genus Lamium (see also Cantino et al., 1997). Therefore, Cantino and Olmstead included the type of this genus, Lamium purpureum, as a specifier for the Lamiina clade. Following Article 11.8 all 27 phylonames include the corresponding rank-based type for genera as specifiers. Among the remaining specifiers, 18 are types of genera in the LSN, but the choice does not seem to result from any particular intension, such as a geographical (taxa from every continent are included) or a historical (oldest described species are not prioritized) bias. In fact, the choices of specifiers that do not form the stem of a phyloname are mainly based on the availability of DNA for phylogenetic analysis. For instance, despite the fact that Callicarpa dichotoma is not the type of the genus Callicarpa, it still represents an important branch in the clade Lamiaceae (Oxelman et al., 2005). This particular species was included in the definition simply because it had been sampled for DNA and sequenced. In many cases names are attached to clades by specifiers from an arbitrary selection, based on subjective personal preferences or our technical abilities to sequence some taxa and not others. In addition, definitions of overlapping and nested taxa should, where possible, use the same reference taxa in order to avoid inflation of specifiers. The bottom line is that the choice of specifiers has a lasting effect on the interpretation of taxon names because they constrain our conceptualization of what we think and talk about in future hypotheses (Härlin, 1998b, 2005; Härlin and Thollesson, 2005). The chosen specifiers will also play a decisive role in selection of taxa for further and future phylogenetic studies.
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Phylogenetic Freedom |
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TopTaxonomic Stability and The...The Quest for Taxonomic...Choice of SpecifiersPhylogenetic FreedomConcluding RemarksAcknowledgmentsReferences |
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Even if the majority of RSN proponents emphasize monophyly, there is no immediate connection between nomenclature and evolutionary relationships in the rank-based system. Consequently, when a Linnaean taxon is shown to be poly-or paraphyletic, this new knowledge does not invalidate the name nor require an automatic revision of the taxon boundaries. Without arguing that this property is desirable, we want to highlight that in RSN we can think and talk about taxa without evolutionary connotations since evolution is at most only an after-the-fact explanation in RSN. In this context, taxa content plays such a prominent role that even the function of name-bearing types is pushed into the background. Let us illustrate the above point with the hypothetical example Aus, which contains the species A, B, and C. Imagine a phylogenetic analysis that includes species B and C (but not A), as well as D and E. D and E constitutes the genus Dus. The analysis reveals that (BC) is the sister group to (DE). Because Aus is conceptualized by its content and no formal nomenclatural modification has been made, (BC) still represents the genus Aus in this phylogenetic context and taxonomists can talk about the genus Aus being sister group to the genus Dus, even without the inclusion of the type of Aus. This is possible because the name Aus only has an implicit "definition" that makes reference to type (A) and rank (genus). That is, with the additional strong focus on taxon content (and no explicit reference to common ancestry), it is still possible to argue that the genus Aus is made up of species A, B, and C. One may of course argue in a similar way that all specifiers of a phyloname do not need to be present in an analysis in order for its extension to be determined—a good taxonomist should know where his or her group of organisms would belong on any phylogenetic tree. And yes, this is true. But it will be at the expense of losing all the explicitness that comes with the introduction of PSN. In other words, although it may be argued (Cantino, personal communication) that it is not necessary for all specifiers to be present in order for a name to be applied, we believe such an argument to severely impoverish the clarity and explicitness of phylogenetic nomenclature. That is, too many applications are possible for each name in a single tree depending on the included specifiers. This hampers taxonomic end users. So, by picking (consciously or unconsciously) your specifiers (out of the list of specifiers) to include in a phylogenetic analysis, you practically decide what the name will refer to¡ The risk of the same name being used for different extensions increases and the problem of taxonomic sameness (Härlin, 1998b, 2003, 2005; Härlin and Thollesson, 2005) needs to be addressed. This suggests that the door is wide open for ambiguity and thus threatening the very reason for moving from RSN to PSN.
Phylogenetic nomenclature, on the other hand, highlights common ancestry and is basically agnostic on taxon content with the exception of the included specifiers (Bryant and Cantino, 2002; but see Härlin, 2003, 2005; Härlin and Thollesson, 2005). Hence, here the fundamental interaction is no longer the link between name and content, but between name and phylogenetic context. Adopting this perspective has consequences on the freedom of the phylogeneticist. Indeed, early choices of specifiers are actually constraining further phylogenetic studies (Härlin, 2005) and once a name is defined, its corresponding specifiers need to be included in the analysis in order to explicitly recognize the clade and to meaningfully apply the name. A flow chart illustrates the intimate interactions between phylogeny and nomenclature in the PSN (Fig. 2). According to this framework, a phylogenetic analysis must precede any nomenclatural issues. Based on the first tree (phylogenetic hypothesis), names are attached to clades through appropriate specifiers (Cladia is defined with a node-based definition with A and D as specifiers). From now on, if one wants to speak about Cladia, for instance in the investigation of its sister clade, A and D must be part of the data matrix. If not, phylogenetic nomenclature loses much of its potential explicitness. The current focus on taxonomic stability that suggests the use of multiple specifiers also forces users of the PSN to include more taxa in their phylogenetic analysis in order to explicitly recognize the extension of particular taxa. Thus, multiple specifiers add a constraint to phylogenetic practice that tends to compromise the phylogenetic freedom of the choice of which taxa to include in an analysis.
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As we have defined it, high universality implies that taxon names are applicable in a wide range of contexts. Consequently, the choice of specifiers should preferably attract both phylocode and nonphylocode adepts in order to maximize the applicability of phylonames. Multiple specifiers constitute a hindrance, because in many cases only a fraction of the specifiers will be part of future (and past) phylogenetic analyses and thus this practice tend to decrease the communication value of phylonames.
Accordingly, attention should be focused on clarity and universality rather than taxonomic stability. Therefore specifiers should be chosen among well-known taxa (in many cases types of genera and of families possess such a property), which are readily available for phylogenetic studies. It implies that specifiers should be easily accessible and for extant taxa it should be possible to sequence them without too many difficulties. Another recommendation, inspired by the Soritacea example, is derived from the common practice in phylogenetics, which often do not combine molecular data with data derived from fossil specimens. Systematists should restrain themselves from coining phylogenetic definitions with both extinct and extant specifiers. But here, like for the rest of the recommendations, its importance is context dependant. For example, there are no valid reasons to exclude Archaeopteryx from a definition for the smallest clade of winged, flying dinosaurs that includes extant specifiers (Laurin, personal communication). However, in cases where most clades are discovered on the basis of neontological characters, the simultaneous use of living and fossil specifiers in definitions may affect phylonames applicability.
Finally, the problem with apomorphy-based definitions with respect to molecular trees could paradoxically be improved by the adoption of a PSN. The current separation between molecular and morphological evolution is untenable and results in partitioning evolutionary studies between gene trees and species phylogenies. The renewed interest in nomenclature is triggering a simultaneous renewal in taxonomy.
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Concluding Remarks |
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TopTaxonomic Stability and The...The Quest for Taxonomic...Choice of SpecifiersPhylogenetic FreedomConcluding RemarksAcknowledgmentsReferences |
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With the introduction of PSN we get two potential advantages; explicitness and a primary focus on evolutionary history rather than ranks and taxon content. Both taxonomists and users of taxonomies should benefit from this. Taxonomists get tools to attach names to evolutionary histories in an explicit way and users of taxonomies may search databases for sequences and trees and retrieve explicit taxonomic information for comparative purposes. Hence, subjective nomenclatural issues may decrease while explicit phylogenetic information becomes easier to handle (e.g., Hibbett et al., 2005).
In order for this scenario to come true, we think that the PSN need to restrict itself to use only two specifiers (or at least as few as possible). If fewer, we are back close to a RSN in terms of a traditional nomenclatural type. If more, the applicability and universality (as discussed above) of these names is severely hampered. So, as we see it, the PSN is at a crossroad. It either will continue to make concessions with the risk to lose its soul (Pickett, 2005; but see Laurin et al., 2005), or it will demonstrate that it outperforms the RSN in practice on the issues of clarity, nomenclatural stability, and universality. Only the future will tell, but achieving taxon content stability by increasing number of specifiers clearly tends to compromise the universality and applicability of phylonames.
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Acknowledgments |
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TopTaxonomic Stability and The...The Quest for Taxonomic...Choice of SpecifiersPhylogenetic FreedomConcluding RemarksAcknowledgmentsReferences |
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We are grateful to Phil Cantino, Matt Haber, Michel Laurin, and Fredrik Pleijel for reading an earlier draft and providing many insightful comments that improved the manuscript. Associate editors Michael Lee and Richard Olmstead reviewed the manuscript and we thank them, as well as editor Roderic Page, for constructive and good comments that helped to clarify our views.
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References |
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