A review of criticisms of phylogenetic nomenclature: is taxonomic freedom the fundamental issue?

The proposal to implement a phylogenetic nomenclatural system governed by the PhyloCode), in which taxon names are defined by explicit reference to common descent, has met with strong criticism from some proponents of phylogenetic taxonomy (taxonomy based on the principle of common descent in which only clades and species are recognized). We examine these criticisms and find that some of the perceived problems with phylogenetic nomenclature are based on misconceptions, some are equally true of the current rank-based nomenclatural system, and some will be eliminated by implementation of the PhyloCode. Most of the criticisms are related to an overriding concern that, because the meanings of names are associated with phylogenetic pattern which is subject to change, the adoption of phylogenetic nomenclature will lead to increased instability in the content of taxa. This concern is associated with the fact that, despite the widespread adoption of the view that taxa are historical entities that are conceptualized based on ancestry, many taxonomists also conceptualize taxa based on their content. As a result, critics of phylogenetic nomenclature have argued that taxonomists should be free to emend the content of taxa without constraints imposed by nomenclatural decisions. However, in phylogenetic nomenclature the contents of taxa are determined, not by the taxonomist, but by the combination of the phylogenetic definition of the name and a phylogenetic hypothesis. Because the contents of taxa, once their names are defined, can no longer be freely modified by taxonomists, phylogenetic nomenclature is perceived as limiting taxonomic freedom. We argue that the form of taxonomic freedom inherent to phylogenetic nomenclature is appropriate to phylogenetic taxonomy in which taxa are considered historical entities that are discovered through phylogenetic analysis and are not human constructs.     

Taxonomie, écologie et lutte biologique

Summary It is impossible to study modern taxonomy without taking into consideration the population genetic and ecology. Thé Linnean concept of monotypic species should be replaced by the biometric study of the frequency of the variability of the biological characters (particularly morphological) used in taxonomy. The study of populations offers a larger scientific interest than the one of isolated types. It gives the possibility of caracterizing the evolution stability of the species. So, Taxonomy can help considerably in biological control. By revealing large variability species, it gives a criterion of their adjusting plasticity. But, by definition, the biological control is based on the adjusting capacity of the entomophagous insects either to a new host or to a new environment. Information given by the taxonomist on the species stability has consequently a great value in the choice and use of the Entomophagous insects. — Ecologists using biological control, expect from the taxonomist to lie more than a label, which implies the use of biometric analysis methods in Entomophagous taxonomy.      

Plant DNA barcoding in China

Identification is the keystone of biology (Bell, 1986).However, to biologists and students of biology, the total numbers of species that must be identified far outnumber the names commonly used in English, Chinese, or other living languages.In addition, the identification cues vary greatly between different taxonomical groups.Even for the taxonomists with long training and experience, it is difficult to remember all specific terms for a given group, e.g., Orchidaceae or Poaceae, without help of floristic books or monographs.It takes much time and effort to train a taxonomist, at a time when fewer and fewer young students are interested in this "classical" and "out-of-style", but extremely important, discipline.Many students elect to learn the more "advanced' and "modem" biological disciples like molecular biology and biochemistry.Thus, in China and therest of the world, taxonomists are themselves becoming "endangered".The rise of the DNA barcoding is expected to mitigate, at least in part, this dilemma.     

蚁蛉科分类研究概况

回顾了世界蚁蛉科 2 0 0多年的分类研究历史。将科的分类研究进程依据年代先后分成 3个阶段 ,并对每个阶段分类研究的代表人物及所取得的成就做了介绍。以列表方式阐述了 1 899年以来所采用过的及目前普遍接受的分类系统。同时对世界蚁蛉科、属、种分布做了说明。最后介绍了中国蚁蛉科的分类研究     

L'analyse et la synthèse en systématique végétale

Analysis and synthesis have been widely used in systematics since, at least, the XIXth Century. Even now, the four major authors (Cronquist, Dahlgren, Takhtajan, Thorne) of angiosperm systems use “synthetic” to qualify their classifications. This word — synthetic or synthesis — has many different meanings that can create ambiguity. Among these meanings, is there one that can be justifiably used to define biological classifications? Although much more than the following applications can be found in the botanical literature, this paper will mainly deal with six meanings which are still in use in contemporary systematics. A synthetic classification has been understood as a classification built upward, from the lower to the higher categories. If we define synthesis as the operation that starts with elements and proceeds to a whole, then upward classification could be viewed as a synthesis in which the concept of hierarchy plays a primordial role, a role that is not initially a part of synthesis. Moreover, synthesis cannot replace all classificatory processes, and other criteria of taxa must be used in addition to synthesis Historically, synthesis has replaced analysis; the latter being employed by Linnaeus in his sexual system. Indeed, Linnaeus used a divisive method in producing his classification; and since division was seen as synonymous to analysis and recognized as a method that led to artificial taxa, leading French taxonomists Adanson, Lamarck and A.-L. de Jussieu among others, rejected analysis and viewed their classifications as synthetic, i.e., based on the natural method. Therefore, a system of value took place: natural was better than artificial, synthesis better than analysis. Reinforcing the importance of synthesis was the belief in a concept widely accepted at the end of the XVIIIth Century: that of continuity. Linking groups and forming a continuum was a procedure eminently synthetic. Such a procedure, known as “chaining”, produced series or sequences of taxa. Analysis was used solely to express the idea of dichotomous or analytical keys, a Lamarckian innovation that enabled taxonomists to identify plants. But whether classifications are built from lower to higher categories (a synthesis of taxa) or from higher to lower categories (an analysis of taxa), another simultaneous, concomitant movement is implied: with the latter, a synthesis of characters, with the former, an analysis of characters. Therefore, a synthetic classification is nevertheless an analytical classification.Basing groups on resemblance instead of difference, results in yet another application of synthesis. This application is probably due to the analogy with “composition”. Already, a separation between resemblance and difference among characters is an analysis. More important, still, is that at a certain rank some characters are used to join whereas, at another rank, they separate. Thus, depending on ranks and taxa, characters are applied in a synthetic or analytical procedure. Here also, other criteria are needed to support group delimitation.In connection with the upward (synthetic) movement in classifying taxa, the use of a great number of characters was also considered to be synthesis. This has been a recurring theme in taxonomy over the last two centuries and was sometimes seen as the Gilmourian approach to classification. When would we be justified to talk about synthesis? After how many characters? In fact, it is not the number of characters that matters but how characters are handled. The use of many characters has been closely linked to the idea of natural groups and its joining with synthesis seems to derive from the association of “natural” and “synthetic”.Synthetic classifications equally imply the common idea that they must represent a résumé of information stemming from all biological fields or disciplines. If classifications portray evolution, as many systematists suggest, then it cannot be just a résumé. And one must first decide what classifications are about: a controversial subject among different schools of thought in taxonomy. This explains another meaning attached to synthesis. Biological classifications have been said to be a synthesis or résumé of two types of information: that of similarity and that of phylogeny. Anagenesis is sometimes viewed as incremental to classification and makes up for a third type of information. Even though taxonomists would (for once!) agree that a classification should be based on phenetic, cladogenetic and anagenetic data, such a classification cannot qualify as a synthesis since it is not a composition and does not meet the definition given above (an operation that starts with elements and goes on to a whole). It is impossible to represent these three types of data together in one classification scheme; they express three, sometimes irreducible, points of view. For such a classification, the word “eclectic” is preferable and closer to reality.The use of synthesis as one term of the dialectical movement has made hesitant steps in taxonomy. Indeed, the two opposed theses that evolve into the synthesis are hardly met in classification and the “dialectical” synthesis promulgated by a few taxonomists can be referred back to synthesis as a résumé.Is classification synthetic because it appears to be based on inductive procedures, as it is sometimes implied by different authors who link deduction and analysis (stemming from downward classification)? In logic, synthesis is sometimes (and questionably so) associated with deduction. Moreover, synthesis cannot follow from induction which deals, for example, with the universality of characters. In that sense, there is no composition and so no synthesis. Thus, although induction has been part of classification, it is not a synthetic method.Apart from the ambiguity originating from the multiple meanings of the word “synthesis” in the context of taxonomy, synthetic classifications do not fully express all the complexity and procedures that lead to it. Actually, a classification is as much a synthesis as an analysis. Both methods are complementary, and should not be opposed as is sometimes the case. This opposition was implicit in the debate between Linneans and Jussieans, surrounding the development of the natural method. If one wants to use “synthetic”, then one should be explicit about its meaning. Taxonomists should also be aware of the incompleteness of synthesis in constructing a classification and should be careful not to create a system of value based upon philosophical ground. They should always prefer a complementary mode of thinking when feasible, instead of an “either-or” approach.     

SPECIES CONCEPTS IN THE GENUSUSNEA(LICHENIZED ASCOMYCETES)

Practically most of the taxonomists working on vascular plants and fungi are using the so-called taxonomic species concept, relying largely on morphological criteria or other observable patterns of discontinuity and assuming that these patterns are reflecting the underlying genetic integrity of species. Such a concept is described in detail here for the genusUsnea. The typological view versus the populational view of species are discussed. The diagnostic value of characters used by previous and recent taxonomists of the genus is analysed. The fact thatUsneahas such a bad taxonomic reputation is discussed. The use by J. Motyka, author of the world monograph published in the thirties, of characters that are strongly modified by environmental factors together with a typological view of species are thought to be mainly responsible for this. More than 770 names have been published worldwide so far and it is suggested that around 50% are to be considered as synonyms.     

On the reality of local and ecological races in lymnaeid snails (Mollusca,Gastropoda, Lymnaeidae)

The reality of ecological and local races was investigated in two widespread Palearctic species of lymnaeid snails (Lymnaea stagnalis and Radix auricularia). Several methods of statistical analysis were used, including two-way ANOVA, cluster analysis, and discriminant analysis for six plastic shell characters. It was shown that none of the methods used could convincingly demonstrate that ecological and local races were present in the studied species. Even in cases when statistically significant differences among the populations in the morphology of shells were revealed, these differences were very small and did not correspond to the meaning that was put into the concept of “race” by malacologists in the past. Perhaps, the formation of such races in pond snails is possible only in case of populations being formed in suboptimal conditions, for example, in thermal springs or at large depths. This being the case, the distinguishing of races requires using other shell characters, both quantitative and qualitative ones.     

On the Other "Phylogenetic Systematics"

De Queiroz and Gauthier, in a serial paper, argue that biological taxonomy is in a sad state, because taxonomists harbor "widely held belief" systems that are archaic and insufficient for modern classification, and that the bulk of practicing taxonomists are essentialists. Their paper argues for the scrapping of the current system of nomenclature, but fails to provide specific rules for the new "Phylogenetic Systematics"—instead we have been presented with a vague and sketchy manifesto based upon the assertion that "clades are individuals" and therefore must be pointed at with proper names, rather than diagnosed by synapomorphies. They claim greater stability for "node pointing," yet even their own examples show that the opposite is true, and their node pointing system is only more stable in a purely metaphysical sense detached from characters, evidence, usage of names, and composition of groups. We will show that the node pointing system is actually far LESS stable than the existing Linnaean System when stability is measured by the rational method of determining the net change in taxa (species) included in a particular group under different classifications.     

Systematics is crucial for the traditional Chinese medicinal studies and industry of macrofungi

Recently, it has been indicated that systematics is of no value to the traditional Chinese medicinal studies and industry of macrofungi. As a fungal taxonomist, I use three genera of the most famous medicinal macrofungi, viz. Sanghuangporus, Ganoderma and Ophiocordyceps, as examples to rebut this opinion. Generally, the well-established systematics are helpful in using correct Latin names for fungal species in medicinal studies; furthermore, the resulting medicinal functions can be exactly matched to a particular species; finally, the particular species can be applied for permissions of utilization in traditional Chinese medicinal industry. Therefore, systematics is crucial for unlocking the potential of macrofungi as valuable resources to be developed in the traditional Chinese medicinal studies and industry, and should continue to be of interest to not just fungal taxonomists but also biochemists, pharmacists and businessmen.     

Near-infrared spectroscopy (NIRS) for taxonomic entomology: A brief review

For over two decades, near-infrared spectroscopy (NIRS) has been applied to a wide spectrum of problems in the field of insect taxonomy. It provides a rapid, non-destructive and relatively cheap method of metabolomic profiling, which can often be used to discriminate closely related species in the same genus. Furthermore, very little training or entomological knowledge is required to operate the instrument. However, a taxonomist is still required to ensure accurate identification of samples used for NIRS model creation and validation. To date, most research has focused on species of economic or epidemiological importance, such as mosquitoes, flies or stored product pests. However, an increasing number of studies are applying NIRS for entomological research with a purely “academic” purpose. As research continues in this field, NIRS has the potential to become more widely accepted in entomology, allowing for the rapid metabolomic profiling of thousands of species.     

Molekulare und., adaptive Evolution, Kladistik und Stammesgeschichte1: Ergänzungen zu einer Arbeitshypothese

Molecular and “adaptive” evolution, cladistic and phylogeny. Supplementations to a working hypothesis The methods of molecular biology and morpholo for the taxonomical assessment have given in several cases very different results. The following examples are discussed: Ailuropoda melanoleuca as an ursoid member of the Carnivora (Ursidae or Ailuropodidae?), Homo saiens and his position to the African apes (Pan and Gorilla) (Pongidae or Hominidae?), Theroipithecus gelada and its affinities to the baboons (Papionini or Theropithecini ?) and Oreopithecus bambolii from the late Miocene of Italy and its taxonomical position within the catarrhine primates. For the three extant species not only the “two level evolution” (molecular and morphological-adaptative evolution) is evident, but also the working hypothesis, that the “adaptative” evolution is more rapidly as the molecular evolution, as the author is suggesting since 1969. The results of molecular methods (immunoloy, amino acid sequences, electrophoresis, DNA-DNA hybridization) are more important for the phylogeny than for the taxonomy. For the cladistic method it is clear, that a cladogram is not a phylogenetic tree, as suggested Peter Ax (1984).     

Cryptic or pseudocryptic: can morphological methods inform copepod taxonomy? An analysis of publications and a case study of the Eurytemora affinis species complex

Interest in cryptic species has increased significantly with current progress in genetic methods. The large number of cryptic species suggests that the resolution of traditional morphological techniques may be insufficient for taxonomical research. However, some species now considered to be cryptic may, in fact, be designated pseudocryptic after close morphological examination. Thus the “cryptic or pseudocryptic” dilemma speaks to the resolution of morphological analysis and its utility for identifying species. We address this dilemma first by systematically reviewing data published from 1980 to 2013 on cryptic species of Copepoda and then by performing an in‐depth morphological study of the former Eurytemora affinis complex of cryptic species. Analyzing the published data showed that, in 5 of 24 revisions eligible for systematic review, cryptic species assignment was based solely on the genetic variation of forms without detailed morphological analysis to confirm the assignment. Therefore, some newly described cryptic species might be designated pseudocryptic under more detailed morphological analysis as happened with Eurytemora affinis complex. Recent genetic analyses of the complex found high levels of heterogeneity without morphological differences; it is argued to be cryptic. However, next detailed morphological analyses allowed to describe a number of valid species. Our study, using deep statistical analyses usually not applied for new species describing, of this species complex confirmed considerable differences between former cryptic species. In particular, fluctuating asymmetry (FA), the random variation of left and right structures, was significantly different between forms and provided independent information about their status. Our work showed that multivariate statistical approaches, such as principal component analysis, can be powerful techniques for the morphological discrimination of cryptic taxons. Despite increasing cryptic species designations, morphological techniques have great potential in determining copepod taxonomy.     

Allozyme characterisation of four Mediterranean evergreen oak species

Polymorphism at 11 enzyme loci was used to compare the four evergreen oak species of the Mediterranean Basin and to establish their taxonomical relationships. As a comparison, two evergreen oak species from Tibet, located in the primary distribution area of evergreen oaks, were analysed at the same loci. Cladistic analyses led to the separation of a cluster of four species, namely the three Mediterranean Q. ilex, Q. coccifera and Q. alnifolia and the Tibetan Q. aquifolioides. The other Tibetan species, Q. semicarpifolia, and Q. suber, from the Western Mediterranean Basin, were very distinct genetically from the four other species. These results were not consistent with previous taxonomical treatment, based on morphology alone, which classified Q. ilex and Q. coccifera in “ilex group” (=subgenus Sclerophyllodrys O. Schwartz), and the other four species in “cerris group” (subgenus Cerris, according to Schwartz). Allozyme variation has thus provided useful information to clarify the taxonomy of evergreen oaks.     

Taxonomy and conservation: a tale of two tinamou species groups (Tinamidae,Crypturellus)

Species delimitation has important consequences for the management of endangered species. Species‐level taxonomy in the genus Crypturellus (Tinamidae) has been based largely on plumage characters and species limits in several groups have been difficult to establish. Because some of the forms of uncertain taxonomic status are currently threatened with extinction, a basic understanding of species limits is crucial not only for taxonomists but also for conservation biologists and managers. We analysed vocal variation to assess species limits in two Crypturellus species‐groups, the red‐legged complex (Crypturellus erythropus and allied forms) and the brown tinamou Crypturellus obsoletus. In the red‐legged complex, where several species‐level taxa have been recognized by some authors, there is no obvious geographic variation in vocalizations and populations appear mostly continuously distributed, with plumage variation largely explicable in terms of environmental conditions. In the brown group, a single species is recognized, but we found marked geographic variation in vocalizations and populations have disjunct distributions; we propose that at least one of the populations in this group likely merits recognition as a separate species. We conclude that incomplete knowledge of patterns of variation in relevant traits in addition to the momentum carried by traditional taxonomy may potentially mislead conservation actions.     

Assessing the taxonomic resolution of southern African trapdoor spiders (Araneae: Ctenizidae; Cyrtaucheniidae; Idiopidae) and implications for their conservation

Taxonomic classifications simultaneously represent hypotheses of taxon identity and relationships to taxonomists, and real, unchanging entities to users of taxonomic information. Taxonomic changes, while representing scientific progress, can be a source of frustration for users. A method for assessing confidence in the taxonomy of a group of organisms would assist users of the taxonomy. A method is presented for determining the degree of development of a taxonomy, a concept termed ‘taxonomic resolution’. The method was applied to six groups of southern African mygalomorph trapdoor spiders, namely Stasimopus Simon 1892 (Ctenizidae Thorell 1877), Ancylotrypa Simon 1889 (Cyrtaucheniidae Simon 1889), four genera of Idiopidae Simon 1889 assessed as a single group, Galeosoma Purcell 1903, the families Migidae Simon 1889 and Microstigmatidae Roewer 1942, and the burrowing scorpion genus Opistophthalmus C. L. Koch 1837 (Scorpionidae Latreille 1802). The method was based on the assumption that species delimitation in a group of organisms, the taxonomy of which is based on morphological characters, depends on whether the sample of material examined is adequate for assessing variation in those characters. Five assessment criteria were identified and scored for a group of species using the taxonomic literature. Estimates of the number of species remaining to be discovered and described in each group were also included in the assessment. The results obtained for the trapdoor spiders ranged from 15 to 29%, indicating a potentially significant degree of uncertainty in the taxonomy. Results for Migidae and Microstigmatidae were 51 and 78% respectively, whereas the result for Opistophthalmus was 93%. The applied value of a measure of taxonomic resolution, the limitations of the method, and a strategy for developing a more generally applicable method are discussed.     

The Species Concept as a Cognitive Tool for Biological Anthropology

Taxonomy is caught between the search for the “perfect” theory and an elusive biological variability. The lack of major advances in issues related to how “species” and other taxonomic categories are defined suggests that perhaps we should avoid excessively rigid formalism in this regard. The risk is a separation between elegant but useless theories and confusing applications of the taxonomic tools. Communication is one of the main functions of taxonomy, and stability one of the main parameters that taxonomy users should be sensitive to. An excess of stability may generate anachronistic consequences while continuous revisions may make the tool of taxonomy scarcely practical. The current tendency pushes toward more and more fragmentation of biologically valid taxa. While taxonomy specialists enjoy such challenges, many taxonomy users feel a bit nervous and discouraged when trying to use a tool that is constantly changing. Debates over taxonomy would seem particularly unrewarding for fields with limited samples and scarce biological diversity, such as palaeoanthropology. In this context, where the information available is rarely sufficient to supply consistent taxonomical evidence, there are frequently excessive efforts to create debate on species separations. The risk is that we maintain the debate on a purely theoretical level, or else we distrust a reliable use of taxonomy. A compromise (and recommended) choice between these two extremes would be to rely on shared and reasonable interpretations of homogeneous evolutionary units, without diving into fine‐grained issues that will remain, however, unresolved. Taxonomy should be a tool, not the goal, of the evolutionary biologist. Our mind needs discrete and recognizable objects to structure our perception of reality. There is no reason to expect that nature works the same way. Am. J. Primatol. 75:10‐15, 2013. © 2012 Wiley Periodicals, Inc.     

After 7 years and 1000 citations: comparative assessment of the DNA barcoding and the DNA taxonomy proposals for taxonomists and non-taxonomists

In 2003, two different approaches-DNA taxonomy and DNA barcoding-were simultaneously proposed to overcome some of the perceived intrinsic weaknesses of the traditional morphology-based taxonomical system, and to help non-taxonomists to resolve their crucial need for accurate and rapid species identification tools. After 7 years, it seems unlikely that a completely new taxonomical system based on molecular characters only (DNA taxonomy) will develop in the future. It is more likely that both morphological and molecular data will be simultaneously analyzed, developing what has been coined as "integrative taxonomy". Concerning DNA barcoding, it is now clear that it does not focus on building a tree-of-life nor to perform DNA taxonomy, but rather to produce a universal molecular identification key based on strong taxonomic knowledge that is collated in the barcode reference library. The indisputable success of the DNA barcoding project is chiefly due to the fact that DNA barcoding standards considerably enhance current practices in the molecular identification field, and standardization offers virtually endless applications for various users.