Should taxon names be explicitly defined?

Overviews are provided for traditional and phylogenetic nomenclature. In traditional nomenclature, a name is provided with a type and a rank. In the rankless phylogenetic nomenclature, a taxon name is provided with an explicit phylogenetic definition, which attaches the name to a clade. Linnaeus’s approach to nomenclature is also reviewed, and it is shown that, although the current system of nomenclature does use some Linnaean conventions (e.g., certain rank-denoting terms, binary nomenclature), it is actually quite different from Linnaean nomenclature. The primary differences between traditional and phylogenetic nomenclature are reviewed. In phylogenetic nomenclature, names are provided with explicit phylogenetic definitions, whereas in traditional nomenclature names are not explicitly defined. In phylogenetic nomenclature, a name remains attached to a clade regardless of how future changes in phylogeny alter the clade’s content; in traditional nomenclature a name is not “married” to any particular clade. In traditional nomenclature, names must be assigned ranks (an admittedly arbitrary process), whereas in phylogenetic nomenclature there are no formal ranks. Therefore, in phylogenetic nomenclature, the name itself conveys no hierarchical information, and the name conveys nothing regarding set exclusivity. It is concluded that the current system is better able to handle new and unexpected changes in ideas about taxonomic relationships. This greater flexibility, coupled with the greater information content that the names themselves (i.e., when used outside the context of a given taxonomy or phytogeny) provide, makes the current system better designed for use by all users of taxon names.     

Cladistic information in phylogenetic definitions and designated phylogenetic contexts for the use of taxon names

A phylogenetic definition of a taxon name associates that name with a clade through its reference to a particular ancestor and all of its descendants. Depending on one's perspective, phylogenetic definitions name either clades on the one true, but unknown, phylogeny, or components on cladograms (clades on hypotheses regarding the true phylogeny). Phylogenetic definitions do not contain enough information to identify components without a reference cladogram. As a result, (1) if clades are equated with components on cladograms, a phylogenetic definition may associate a taxon name with different clades on different cladograms, and (2) the inclusiveness, diagnostic synapomorphies, and distribution in time and space of the clade with a particular name can differ markedly depending on the phylogenetic hypothesis one chooses to adopt. This potentially unacceptable lability in the clade to which a name refers can be avoided by using a taxon name in conjunction with only phylogenetic hypotheses on which specific taxa are related in a particular fashion. This designated phylogenetic context can be described in an n-taxon statement that would be appended to the phylogenetic definition. Use of the taxon name would be considered inappropriate in conjunction with cladograms on which the relationships contradict those in the n-taxon statement. Whereas phylogenetic definitions stabilize the meaning of taxon names, designated phylogenetic contexts would stabilize the usage of those names.     

Phylogenetic definitions and taxonomic philosophy

An examination of the post-Darwinian history of biological taxonomy reveals an implicit assumption that the definitions of taxon names consist of lists of organismal traits. That assumption represents a failure to grant the concept of evolution a central role in taxonomy, and it causes conflicts between traditional methods of defining taxon names and evolutionary concepts of taxa. Phylogenetic definitions of taxon names (de Queiroz and Gauthier 1990) grant the concept of common ancestry a central role in the definitions of taxon names and thus constitute an important step in the development of phylogenetic taxonomy. By treating phylogenetic relationships rather than organismal traits as necessary and sufficient properties, phylogenetic definitions remove conflicts between the definitions of taxon names and evolutionary concepts of taxa. The general method of definition represented by phylogenetic definitions of clade names can be applied to the names of other kinds of composite wholes, including populations and biological species. That the names of individuals (composite wholes) can be defined in terms of necessary and sufficient properties provides the foundation for a synthesis of seemingly incompatible positions held by contemporary individualists and essentialists concerning the nature of taxa and the definitions of taxon names.     

Apomorphy-based definition also pinpoints a node, and PhyloCode names prevent effective communication

Acceptable methods of defining taxon (or clade) names in the draft PhyloCode, or so-called phylogenetic nomenclature, are “node based,” “stem based,” and “apomorphy based.” All of them define a clade name by pinpointing a node; whereas node-based and stem-based definitions require two or more taxon “specifiers” to define names, an apomorphy-based definition requires two specifiers of different types; namely, a single-taxon specifier and a character specifier. The taxon specifier in an apomorphy-based definition is completely different from the “type” in the Linnaean system. Taxon (or clade) names in the PhyloCode are characterized in two entirely different manners: One is a name that does not change, either in its orthography or in the contents of the taxon referred to by it (or its meaning) over time; the other is a name that is just like a pure mark and thus has no meaning. Communication through such PhyloCode names is very ineffective or impossible.     

Ceci n'est pas une pipe: names, clades and phylogenetic nomenclature

An introduction is provided to the literature and to issues relating to phylogenetic nomenclature and the PhyloCode, together with a critique of the current Linnaean system of nomenclature. The Linnaean nomenclature fixes taxon names with types, and associates the names with ranks (genus, family, etc.). In phylogenetic nomenclature, names are instead defined with reference to cladistic relationships, and the names are not associated with ranks. We argue that taxon names under the Linnaean system are unclear in meaning and provide unstable group–name associations, notwithstanding whether or not there are agreements on relationships. Furthermore, the Linnaean rank assignments lack justification and invite unwarranted comparisons across taxa. On the contrary, the intention of taxon names in phylogenetic nomenclature is clear and stable, and the application of the names will be unambiguous under any given cladistic hypothesis. The extension of the names reflects current knowledge of relationships, and will shift as new hypotheses are forwarded. The extension of phylogenetic names is, therefore, clear but is associated to (and thus dependent upon) cladistic hypotheses. Stability in content can be maximized with carefully formulated name definitions. A phylogenetic nomenclature will shift the focus from discussions of taxon names towards the understanding of relationships. Also, we contend that species should not be recognized as taxonomic units. The term ‘species’ is ambiguous, it mixes several distinct classes of entities, and there is a large gap between most of the actual concepts and the evidence available to identify the entities. Instead, we argue that only clades should be recognized. Among these, it is useful to tag the smallest named clades, which all represent non-overlapping groups. Such taxa  – LITUs (Least Inclusive Taxonomic Units) – are distinguished from more inclusive clades by being spelled with lower-case initial letter. In contrast to species, LITUs are conceptually straightforward and are, like other clades, identified by apomorphies.     

Species names in phylogenetic nomenclature

Linnaean binomial nomenclature is logically incompatible with the phylogenetic nomenclature of de Queiroz and Gauthier (1992, Annu. Rev. Ecol. Syst. 23:449-480): The former is based on the concept of genus, thus making this rank mandatory, while the latter is based on phylogenetic definitions and requires the abandonment of mandatory ranks. Thus, if species are to receive names under phylogenetic nomenclature, a different method must be devised to name them. Here, 13 methods for naming species in the context of phylogenetic nomenclature are contrasted with each other and with Linnaean binomials. A fundamental dichotomy among the proposed methods distinguishes those that retain the entire binomial of a preexisting species name from those that retain only the specific epithet. Other relevant issues include the stability, uniqueness, and ease of pronunciation of species names; their capacity to convey phylogenetic information; and the distinguishability of species names that are governed by a code of phylogenetic nomenclature both from clade names and from species names governed by the current codes. No method is ideal. Each has advantages and drawbacks, and preference for one option over another will be influenced by one's evaluation of the relative importance of the pros and cons for each. Moreover, sometimes the same feature is viewed as an advantage by some and a drawback by others. Nevertheless, all of the proposed methods for naming species in the context of phylogenetic nomenclature provide names that are more stable than Linnaean binomials.     

Naming diversity in an evolutionary context: Phylogenetic definitions of the Roucela clade (Campanulaceae/Campanuloideae) and the cryptic taxa within

In recent times, evolution has become a central tenet of taxonomy, but nomenclature has consistently been decoupled from the tree‐thinking process, often leading to significant issues in reconciling traditional (Linnaean) names with clades in the Tree of Life. Recent evolutionary studies on the Roucela clade, a group of endemic plants found in the Mediterranean Basin, motivated the establishment of phylogenetic concepts to formally anchor clade names on the Campanuloideae (Campanulaceae) tree. These concepts facilitate communication of clades that approximate traditionally defined groups, in addition to naming newly discovered cryptic diversity in a phylogenetic framework.     

Toward an integrated system of clade names

Although the proposition that higher taxa should correspond to clades is widely accepted, current nomenclature does not distinguish clearly between different clades in nested series. In particular, the same name is often applied to a total clade, its crown clade, and clades originating with various nodes, branches, and apomorphies in between. An integrated system of clade names is described based on categories of clades defined with respect to lineages that have survived to the present time. In this system, the most widely known names are applied to crown clades, the names of total clades are formed by adding a standard prefix to the names of the corresponding crowns, and the names of apomorphy clades describe the specific apomorphies with which they originated. Relative to traditional approaches, this integrated approach to naming clades is both more precise concerning the associations of names with particular clades and more efficient with regard to the cognitive effort required to recognize the names of corresponding crown and total clades. It also seems preferable to five alternatives that could be used to make the same distinctions. The integrated system of clade names has several advantages, including the facilitation of communication among biologists who study distantly related clades, promoting a broader conceptualization of the origins of distinctive clades of extant organisms and emphasizing the continuous nature of evolution.     

Ecological radiation with limited morphological diversification in salamanders

A major goal of evolutionary biology is to explain morphological diversity among species. Many studies suggest that much morphological variation is explained by adaptation to different microhabitats. Here, we test whether morphology and microhabitat use are related in plethodontid salamanders, which contain the majority of salamander species, and have radiated into a striking diversity of microhabitats. We obtained microhabitat data for 189 species that also had both morphometric and phylogenetic data. We then tested for associations between morphology and microhabitat categories using phylogenetic comparative methods. Associations between morphology and ecology in plethodontids are largely confined to a single clade within one subfamily (Bolitoglossinae), whereas variation in morphology across other plethodontids is unrelated to microhabitat categories. These results demonstrate that ecological radiation and morphological evolution can be largely decoupled in a major clade. The results also offer a striking contrast to lizards, which typically show close relationships between morphology and microhabitat.     

Evolutionary relationships within the Neotropical, eusporangiate fern genus Danaea (Marattiaceae)

Genera within the eusporangiate fern family Marattiaceae have long been neglected in taxonomic and systematic studies. Here we present the first phylogenetic hypothesis of relationships within the exclusively Neotropical genus Danaea based on a sampling of 60 specimens representing 31 species from various Neotropical sites. We used DNA sequence data from three plastid regions (atpB, rbcL, and trnL-F), morphological characters from both herbarium specimens and live plants observed in the field, and geographical and ecological information to examine evolutionary patterns. Eleven representatives of five other marattioid genera (Angiopteris, Archangiopteris, Christensenia, Macroglossum, and Marattia) were used to root the topology. We identified three well-supported clades within Danaea that are consistent with morphological characters: the "leprieurii" clade (containing species traditionally associated with the name D. elliptica), the "nodosa" clade (containing all species traditionally associated with the name D. nodosa), and the "alata" clade (containing all other species). All three clades are geographically and ecologically widely distributed, but subclades within them show various distribution patterns. Our phylogenetic hypothesis provides a robust framework within which broad questions related to the morphology, taxonomy, biogeography, evolution, and ecology of these ferns can be addressed.     

Phylogenetic uncertainty revisited: Implications for ecological analyses

Ecologists and biogeographers usually rely on a single phylogenetic tree to study evolutionary processes that affect macroecological patterns. This approach ignores the fact that each phylogenetic tree is a hypothesis about the evolutionary history of a clade, and cannot be directly observed in nature. Also, trees often leave out many extant species, or include missing species as polytomies because of a lack of information on the relationship among taxa. Still, researchers usually do not quantify the effects of phylogenetic uncertainty in ecological analyses. We propose here a novel analytical strategy to maximize the use of incomplete phylogenetic information, while simultaneously accounting for several sources of phylogenetic uncertainty that may distort statistical inferences about evolutionary processes. We illustrate the approach using a clade‐wide analysis of the hummingbirds, evaluating how different sources of uncertainty affect several phylogenetic comparative analyses of trait evolution and biogeographic patterns. Although no statistical approximation can fully substitute for a complete and robust phylogeny, the method we describe and illustrate enables researchers to broaden the number of clades for which studies informed by evolutionary relationships are possible, while allowing the estimation and control of statistical error that arises from phylogenetic uncertainty. Software tools to carry out the necessary computations are offered.     

Phylogenetic position of the adeleorinid coccidia (Myzozoa, Apicomplexa, Coccidia, Eucoccidiorida, Adeleorina) inferred using 18S rDNA sequences

Investigating the evolutionary relationships of the major groups of Apicomplexa remains an important area of study. Morphological features and host-parasite relationships continue to be important in the systematics of the adeleorinid coccidia (suborder Adeleorina), but the systematics of these parasites have not been well-supported or have been constrained by data that were lacking or difficult to interpret. Previous phylogenetic studies of the Adeleorina have been based on morphological and developmental characters of several well-described species or based on nuclear 18S ribosomal DNA (rDNA) sequences from taxa of limited taxonomic diversity. Twelve new 18S rDNA sequences from adeleorinid coccidia were combined with published sequences to study the molecular phylogeny of taxa within the Adeleorina and to investigate the evolutionary relationships of adeleorinid parasites within the Apicomplexa. Three phylogenetic methods supported strongly that the suborder Adeleorina formed a monophyletic clade within the Apicomplexa. Most widely recognized families within the Adeleorina were hypothesized to be monophyletic in all analyses, although the single Hemolivia species included in the analyses was the sister taxon to a Hepatozoon sp. within a larger clade that contained all other Hepatozoon spp. making the family Hepatozoidae paraphyletic. There was an apparent relationship between the various clades generated by the analyses and the definitive (invertebrate) host parasitized and, to lesser extent, the type of intermediate (vertebrate) host exploited by the adeleorinid parasites. We conclude that additional taxon sampling and use of other genetic markers apart from 18S rDNA will be required to better resolve relationships among these parasites.     

Phylogeny of the sabertoothed felids (Carnivora: Felidae: Machairodontinae)

In recent years, advances in our understanding of feline relationships have cast light on their evolutionary history. In contrast, there have been no phylogenetic analyses on machairodont felids, making it difficult to develop an evolutionary hypothesis based on the recent surge of studies on their craniomandibular morphology and functional anatomy. In this paper, I provide the first phylogenetic hypothesis of machairodont relationships based on 50 craniomandibular and dental characters from a wide range of sabercats spanning more 11 Myr. Exact searches produced 19 most‐parsimonious trees, and a strict consensus was well resolved. The Machairodontinae comprise a number of basal taxa (Promegantereon, Machairodus, Nimravides, Dinofelis, Metailurus) and a well‐supported clade of primarily Plio‐Pleistocene taxa (Megantereon, Smilodon, Amphimachairodus, Homotherium, Xenosmilus) for which the name Eumachairodontia taxon novum is proposed. Previous phenetic grouping of machairodont taxa into three distinct groups, the Smilodontini, Homotherini and Metailurini, was not supported by cladistic parsimony analysis, and forcing monophyly of these groups was significantly incompatible with character distribution. Machairodonts as a clade are not characterized by saberteeth, i.e. hypertrophied, blade‐like upper canines, but by small lower canines, as well as small M¹; and large P³ parastyle. True saberteeth arose later and are a synapomorphy of the Eumachairodontia.     

Advantages of naming species under the PhyloCode: An example of how a new species of Discodorididae (Mollusca, Gastropoda, Euthyneura, Nudibranchia, Doridina) may be named

A new species of Discodorididae is described from the Pacific coasts of Mexico and Panama. It is named using a modified version of the epithet-based nomenclature proposed by Url Lanham 40 years ago. The species described here can be placed confidently in the clade Discodorididae, but not in any of its subclades (traditionally taxa of genus rank). The unique, epithet-based name of the species is “aliciae Dayrat, 2005”. The combination Discodorididae aliciae may also be used, once the unique, epithet-based name has been cited. Discodorididae aliciae is an example of how a new species of Discodorididae could be named in the context of phylogenetic nomenclature. I argue that epithet-based species names and their combinations with clade addresses should be very appealing to people who think phylogenetically. I also discuss two advantages of such combinations: first, they should be more stable than Linnaean binomials, which often change for arbitrary (e.g. non-phylogenetic) reasons; second, they should help taxonomists avoid creating multiple names for the same species.     

Phylogenetic relationships in the Neotropical tribe Hamelieae (Rubiaceae,Cinchonoideae) and comments on its generic limits

Our molecular phylogenetic analyses shed some light on the evolutionary relationships within the Hamelieae tribe. Phylogenetic reconstructions based on Internal Transcribed Spacer and trnL-F sequence data revealed the presence of three distinct evolutionary lineages. The first clade includes Hamelia and Syringantha, the second clade includes Deppea s.l. (including Bellizinca, Csapodya, and Edithea), and the third clade includes Pinarophyllon, Deppeopsis, Hoffmannia,Pseudomiltemia, Plocaniophyllon, Omiltemia, and Renistipula. The phylogenetic analysis re-evaluated some taxonomical combinations. The transfer of Deppeopsistaxa from Deppea s.l. is supported, but however, the monophyly of the genus is not. The transfer of Renistipula from Rondeletieae is also highly supported. BothCsapodya and Edithea species form a well-defined group among Deppea s.l. with high posterior probabilities, allowing to reconsider the exclusion or integration of these taxa to Deppea.     

Phylogeny of the lichen genus Placopsis and its allies based on Bayesian analyses of nuclear and mitochondrial sequences

The phylogenetic relationships of the lichen genus Placopsis and related genera in the Agyriales were analyzed using molecular data. We obtained a total of 66 new sequences from the nuclear ITS, LSU and the mitochondrial SSU rDNA. Phylogenetic analyses were conducted in a Bayesian and a maximum-parsimony framework. Our analyses show that Placopsis is paraphyletic with members of Orceolina nesting within the genus. A morphological character supporting the Placopsis-Orceolina clade is the non-amyloid ascus. The section Aspiciliopsis as defined by sunken fruiting bodies is not supported, but the type species of Aspiciliopsis is more closely related to Orceolina. This clade shares apothecia with reduced amphithecia as apomorphic character. We suggest resurrecting the generic name Aspiciliopsis. Trapelia is the sister genus to Placopsis and Aspiciliopsis/Orceolina.     

Taxonomic names and phylogenetic trees

This paper addresses the issue of philosophy of names within the context of biological taxonomy, more specifically how names refer. By contrasting two philosophies of names, one that is based on the idea that names can be defined and one that they cannot be defined, I point out some advantages of the latter within phylogenetic systematics. Due to the changing nature of phylogenetic hypotheses, the former approach tends to rob taxonomy from its unique communicative value since a name that is defined refers to whatever fits the definition. This is particularly troublesome should the hypothesis of phylogenetic relationship change. I argue that, should we decide to accept a new phylogenetic hypothesis, it is also likely that our view of what to name may change. A system where names only refer acknowledge this, and accordingly leaves it open whether to keep a name (and accept the way it refers in the new hypothesis) or discard a name and introduce new names for the parts of the tree that we find scientifically interesting. One of the main differences between a phylogenetic system of definition (PSD) and a phylogenetic system of reference (PSR) is that the former is governed by laws of language while the latter by communicative needs of taxonomists. Thus, a PSR tends to give primacy to phylogenetic trees rather than phylogenetic definitions of names should our views of which phylogenetic hypothesis to accept change. © 1998 The Norwegian Academy of Sciences and Letters     

Phylogenetic overview of Erysiphaceae based on nrDNA and MCM7 sequences

The classification system and evolutionary history of Erysiphaceae have been studied based on the results of molecular phylogenetic analyses. However, the sequence data used for these phylogenetic estimations have been limited to the nrDNA of ca., 50 taxa, and the relationships among higher taxonomic groups are not well understood. To provide a phylogenetic overview of Erysiphaceae, we performed phylogenetic estimations based on nrDNA and MCM7 sequences obtained from ca., 270 taxa. The phylogenetic tree showed a similar topology to the trees obtained in previous studies, although the branching order between Golovinomyceteae and Phyllactinieae was different and Phyllactinieae was not monophyletic. Phyllactinieae and Erysipheae were estimated to diversify after the divergence of Golovinomyceteae, suggesting an evolutionary trend in which non-catenate conidia + endoparasitic or non-catenate conidia + ectoparasitic lineages were derived from catenate conidia + ectoparasitic lineages. Phyllactinieae was divided into a clade of Phyllactinia + Leveillula and other clade(s) consisting of Pleochaeta and Queirozia. The phylogenetic hypothesis of Erysiphaceae was updated based on the largest dataset to date, but the higher-level phylogenetic relationships remain unclear. For a more robust phylogenetic hypothesis of Erysiphaceae, further sequence data, including protein coding regions, should be added to the dataset of nrDNA sequences.