Aphyly: identifying the flotsam and jetsam of systematics

Many taxon names in any classification will be composed of taxa that have yet to be demonstrated as monophyletic, that is, characterized by synapomorphies. Such taxa might be called aphyletic, the flotsam and jetsam in systematics, simply meaning they require taxonomic revision. The term aphyly is, however, the same as, if not identical to, Hennig's “Restkörper” and Bernardi's merophyly. None of these terms gained common usage. We outline Hennig's use of “Restkörper” and Bernardi's use of merophyly and compare it to aphyly. In our view, application of aphyly would avoid the oft made assumption that when a monophyletic group is discovered from within an already known and named taxon, then the species left behind are rendered paraphyletic. By identifying the flotsam and jetsam in systematics, we can focus on taxa in need of attention and avoid making phylogenetic faux pas with respect to their phylogenetic status.     

The use of parsimony in testing phylogenetic hypotheses

With the advance of cladistic theory differences in principle between it and other systematic techniques are few but of fundamental importance. In the mechanics of classification they are confined to ranking and the rejection of paraphyletic taxa. In cladistic analysis, leading to cladograms, trees and phylogeny reconstruction, inconsistencies in apparent synapomorphies are said to be resolved using Popper's hypothetico-deductive method together with the principle of parsi However, not only do cladists not use Popper's methodology, which is inconsistent with parsimony, but their use of parsimony is invalid as a test of phylo The only accepted extrinsic test of a classification is that enunciated by John Stuart Mill. It has been claimed that cladistic classifications yield the best results when judged by Mill's criteria, but this is only possibly the case with analytic classifications produced by numerical techniques. No satisfactory test exists in normal (synthetic) cladism for distinguishing synapomorphy from homoplasy. The effects of this are particularly dire in cladograms and classifications involving fossils in which a Stufenreihe arrangement is adopted.     

Hennig's semaphoront concept and the use of ontogenetic stages in phylogenetic reconstruction

A new practice in systematics, “semaphoront” coding, treats developmental stages as terminals, and it derives from Hennig's concept of the same name. Semaphoront coding has been implemented recently by Lamsdell and Selden (BMC Evol. Biol., 2013, 13:98) and Wolfe and Hegna (Cladistics, 2014, 30:366) in an effort to understand the relationships of fossil taxa of unknown developmental stage. We submit that this approach is antithetical to cladistic practice and constitutes a gross misunderstanding of Hennig's original idea. Here we review the concept of the semaphoront and clarify the role of the semaphoront in phylogenetic systematics. We contend that treating ontogenetic stages as terminals both violates tenets of phylogenetic systematics and oversimplifies the complexity of developmental processes. We advocate Hennig's alternative of including data from as many semaphoronts as possible, but implemented using the superior total evidence framework. Finally, we contend that the application of semaphoront coding to any palaeontological question requires invoking multiple, unjustified assumptions, and ultimately will not yield a possible phylogenetic solution. A total evidence approach can grapple with the placement of fossil developmental stages, if only imperfectly.     

When phylogenetics met biogeography: Willi Hennig,Lars Brundin and the roots of phylogenetic and cladistic biogeography

Willi Hennig's (Beitr. Ent. 1960, 10, 15) Die Dipteren-Fauna von Neuseeland als systematisches und tiergeographisches Problem applied a phylogenetic approach to examine the distributional patterns exhibited by the Diptera of New Zealand. Hennig showed how phylogenetic trees may be used to infer dispersal, based on the progression and deviation rules, and also discussed the existence of vicariance patterns. The most important author who applied Hennig's phylogenetic biogeography was Lars Brundin, when analysing the phylogenetic relationships of two taxa of Chironomidae (Diptera) and using them to examine the biogeographic relationships of Australia, New Zealand, South America and South Africa. The relevance of Brundin's contribution was noted by several authors, as it began the cladistic or vicariance approach to biogeography, that implies the discovery of vicariance events shared by different monophyletic groups. Both phylogenetic and cladistic biogeography have a place in contemporary biogeography, the former for analysing taxon biogeography and the latter when addressing Earth or biota biogeography. The recent use of the term “phylogenetic biogeography” to refer to a posteriori methods of cladistic biogeography is erroneous and should be avoided.     

Epistemic and community transition in American evolutionary studies: the ‘Committee on Common Problems of Genetics,Paleontology, and Systematics’ (1942–1949)

The Committee on Common Problems of Genetics, Paleontology, and Systematics (United States National Research Council) marks part of a critical transition in American evolutionary studies. Launched in 1942 to facilitate cross-training between genetics and paleontology, the Committee was also designed to amplify paleontologist voices in modern studies of evolutionary processes. During coincidental absences of founders George Gaylord Simpson and Theodosius Dobzhansky, an opportunistic Ernst Mayr moved into the project’s leadership. Mayr used the opportunity for programmatic reforms he had been pursuing elsewhere for more than a decade. These are evident in the Bulletins he distributed under Committee auspices. In his brief tenure as Committee leader, Mayr gained his first substantial foothold within the coalescing community infrastructure of evolutionary studies. Carrying this momentum forward led Mayr directly into the project to launch the journal Evolution. The sociology of interdisciplinary activity provides useful tools for understanding the Committee’s value in the broad sweep of change in evolutionary studies during the synthesis period.     

Which Is the Most Suitable Classification for Colorectal Cancer,Log Odds,the Number or the Ratio of Positive Lymph Nodes?

Objective

The aim of the current study was to investigate which is the most suitable classification for colorectal cancer, log odds of positive lymph nodes (LODDS) classification or the classifications based on the number of positive lymph nodes (pN) and positive lymph node ratio(LNR) in a Chinese single institutional population.

Design

Clinicopathologic and prognostic data of 1297 patients with colorectal cancer were retrospectively studied. The log-rank statistics, Cox''s proportional hazards model, the Nagelkerke R² index and a Harrell''s C statistic were used.

Results

Univariate and three-step multivariate analyses identified that LNR was a significant prognostic factor and LNR classification was superior to both the pN and LODDS classifications. Moreover, the results of the Nagelkerke R² index (0.130) and a Harrell''s C statistic (0.707) of LNR showed that LNR and LODDS classifications were similar and LNR was a little better than the other two classifications. Furthermore, for patients in each LNR classification, prognosis was homologous between those in different pN or LODDS classifications. However, for patients in pN1a, pN1b, LODDS2 and LODDS3 classifications, significant differences in survival were observed among patients in different LNR classifications.

Conclusions

For patients with colorectal cancer, the LNR classification is more suitable than pN and LODDS classifications for prognostic assessment in a Chinese single institutional population.     

George Gaylord Simpson as mentor and apologist for paleoanthropology

The influence of George Gaylord Simpson (1902–1984) on paleoanthropology provides a well-documented, historical example of how one scientific discipline can impact upon another, bringing the latter quickly “up to speed” without having to retrace ground covered by the former. Paleoanthropologists were bystanders during the formulation of the evolutionary synthesis (1936–1947). After World War II, the younger paleoanthropologists looked to George Gaylord Simpson as one of several mentors regarding the implications of the synthesis for their own discipline. But why Simpson? Having earlier defined the superfamily Hominoidea (1931) as holding the Pongidae and Hominidae and monographed lower primate fossils (e.g., “Studies on the earliest primates,” 1940), Simpson's “Principles of classification and a classification of mammals” (1945) further solidified his reputation as a mammalian systematist. Simpson's Meaning of Evolution (1949) was widely read as an introduction to the synthesis, and his Tempo and Mode in Evolution (1944) made accessible the more complex aspects. Consequently, in the 1950s and 1960s paleoanthropologists invited Simpson to participate in their symposia (e.g., “Some principles of historical biology bearing on human origins,” 1951; “The meaning of taxonomic statements,” 1964), used his books as classroom texts, and cited his publications to support claims for their own work. Later in the 1960s, Simpson moved from mentor to apologist, as the paleoanthropologists were by then familiar with the synthesis and incorporated its theoretical concepts in their interpretations of the many newly discovered hominoid fossils. Simpson now took special care to celebrate these results in his more general, less technical writings, acting as a forceful apologist for the materialistic view of human origins (e.g., “The biological nature of man,” 1966; “The evolutionary concept of man,” 1972). During the 1970s, Simpson's influence waned, and he became just another practitioner at the margin of the discipline. However, anthropologists acknowledged Simpson's earlier impact, for example, when he was invited, yet again, to address them at the 50th anniversary celebration of the American Association of Physical Anthropologists in 1981.     

Evaluating the stability of the classification of community data

We propose a method for a posteriori evaluation of classification stability which compares the classification of sites in the original data set (a matrix of species by sites) with classifications of subsets of its sites created by without‐replacement bootstrap resampling. Site assignments to clusters of the original classification and to clusters of the classification of each subset are compared using Goodman‐Kruskal's lambda index. Many resampled subsets are classified and the mean of lambda values calculated for the classifications of these subsets is used as an estimation of classification stability. Furthermore, the mean of the lambda values based on different resampled subsets, calculated for each site of the data set separately, can be used as a measure of the influence of particular sites on classification stability. This method was tested on several artificial data sets classified by commonly used clustering methods and on a real data set of forest vegetation plots. Its strength lies in the ability to distinguish classifications which reflect robust patterns of community differentiation from unstable classifications of more continuous patterns. In addition, it can identify sites within each cluster which have a transitional species composition with respect to other clusters.     

A botanical critique of cladism

Clade versus grade is an old question in taxonomy, going back as far as Darwin himself. Taxonomists have long believed that both must be taken into account in the formation of a general-purpose system. Recently clade has been elevated to a position of total dominance by a group of taxonomists who take their inspiration from Willi Hennig. Mayr has dubbed this approach cladism, and its exponents cladists. Cladistic theory is being vigorously developed and propounded by Hennig’s disputatious disciples, and much of the present-day theory would scarcely be recognized by the founder. I here address myself to what I consider the core features of present-day cladism. The essential distinctive feature of cladism, and its fatal flaw, is that a group is considered to be monophyletic, and thus taxonomically acceptable, only if it includesall the descendants from the most recent common ancestor. The traditional taxonomic view has been that a group can still be considered monophyletic (and thus taxonomically acceptable) after some of its more divergent branches have been trimmed off. This simple and seemingly innocuous difference has profound consequences to the taxonomic system. In Hennigian classification, organisms are ranked entirely on the basis of recency of common descent, that is, on the basis of the sequence of dichotomies in the inferred phylogeny. Theamount of divergence scarcely enters into the picture. This procedure represents an effort to capture taxonomy for a narrowly limited special purpose, at the expense of the important and necessary function of providing a general-purpose system that can be used by all who are concerned with similarities and differences among organisms. The first corollary of the Hennigian concept of phylogenetic taxonomy is that no existing taxon can be ancestral to any other existing taxon. The descendant must be included in the same taxon as its ancestor. At the level of species this is palpably false. The ancestral species often continues to exist for an indefinite time after giving rise to one or more descendants. At the higher taxonomic levels adherence to the principle often requires excessive lumping or excessive splitting to avoid paraphyletic groups (i.e., groups that do not include all of their own descendants), and it forbids the taxonomic recognition of many conceptually useful groups. Neither the prokaryotes nor the dicotyledons form a cladistically acceptable taxon, since both are paraphyletic. The prokaryotes are putatively ancestral to the eukaryotes, and the dicotyledons are putatively ancestral to the monocotyledons. Many other traditional and readily recognizable taxa would have to be abandoned, without being replaced by conceptually useful groups. Fossils present a special problem, because the whole concept of cladistic classification depends on the absence of taxa at the branch points of the cladogram. Presumably all of these branch points were at some time in the past represented by actual taxa, which under cladistic theory can neither be assigned to one of their descendants nor treated as paraphyletic taxa. The difficulty is mitigated somewhat by the gaps in the known fossil record. Once it is admitted that paraphyletic as well as holophyletic groups are taxonomically acceptable, there is much value in cladistic methodology. Formal outgroup comparison for the establisment of polarity, and the emphasis on synapomorphies in the construction of a cladogram can both be usefully incorporated into taxonomic theory and practice. These require no revolution in taxonomic thought. There are unresolved problems, however, in how to gather and manipulate the data, and how to interpret the cladogram produced by computers. In any complex group, the computer may produce several or many cladograms of equal or nearly equal parsimony. This is particularly true in angiosperms, among which the extensive evolutionary parallelism casts doubt on the importance of parsimony and may lead to the production of hundreds of such cladograms for a single group. Despite the claims of objectivity and repeatability in cladistic taxonomy, the necessity for some subjective decisions remains. The Wagner groundplan-divergence method has most of the advantages of formal cladism without the most important disadvantages. Wagner accepts paraphyletic taxa in principle, and he casts a wider net for data bearing on the polarity of characters. In complex groups consisting of many taxa, however, both methods retain a strong subjective component in the computer manipulation and in the degree of reliance on absolute parsimony.     

Finding the Minimum Sample Richness (MSR) for multivariate analyses: implications for palaeoecology

Many techniques have been developed to estimate species richness and beta diversity. Those techniques, dependent on sampling, require abundance or presence/absence data. Palaeontological data is by nature incomplete, and presence/absence data is often the only type of data that can be used to provide an estimate of ancient biodiversity. We used a simulation approach to investigate the behaviour of commonly used similarity indices, and the reliability of classifications derived from these indices, when working with incomplete data. We drew samples, of varying number and richness, from artificial species lists, which represented original life assemblages, and calculated error rates for classifications of the parent lists and samples. Using these results, we estimated the Minimum Sample Richness (MSR) needed to achieve 95% classification accuracy. Results were compared for classifications derived from several commonly used similarity indexes (Dice, Jaccard, Simpson and Raup–Crick). MSR was similar for the Dice, Jaccard and Simpson indices. MSR for the Raup–Crick index was often much lower, suggesting that it is preferable for classifying patchy data, however the performance of this index was less stable than the other three in the simulations, which required an even lower MSR. MSR can be found for all presence/absence data from the contour graphs and equations as long as the absolute species richness and the beta diversity can be estimated.     

Mayr's view of Darwin: was Darwin wrong about speciation?

We commonly read or hear that Charles Darwin successfully convinced the world about evolution and natural selection, but did not answer the question posed by his most famous book, ‘On the Origin of Species …’. Since the 1940s, Ernst Mayr has been one of the people who argued for this point of view, claiming that Darwin was not able to answer the question of speciation because he failed to define species properly. Mayr undoubtedly had an important and largely positive influence on the study of evolution by stimulating much evolutionary work, and also by promoting a ‘polytypic species concept’ in which multiple, geographically separated forms may be considered as subspecies within a larger species entity. However, Mayr became seduced by the symmetry of a pair of interlocking ideas: (1) that coexistence of divergent populations was not possible without reproductive isolation and (2) reproductive isolation could not evolve in populations that coexist. These beliefs led Mayr in 1942 to reject evidence of the importance of intermediate stages in speciation, particularly introgression between hybridizing species, which demonstrates that complete reproductive isolation is not necessary, and the existence of ecological races, which shows that ecological divergence can be maintained below the level of species, in the face of gene flow. Mayr's train of thought led him to the view that Darwin misunderstood species, and that species were fundamentally different from subspecific varieties in nature. Julian Huxley, reviewing similar data at the same time, came to the opposite conclusion, and argued that these were the intermediate stages of speciation expected under Darwinism. Mayr's arguments were, however, more convincing than Huxley's, and this caused a delay in the acceptance of a more balanced view of speciation for many decades. It is only now, with new molecular evidence, that we are beginning to appreciate more fully the expected Darwinian intermediates between coexisting species. © The Author. Journal compilation © 2008 The Linnean Society of London, Biological Journal of the Linnean Society, 2008, 95 , 3–16.     

Evaluation of syntaxonomic schemes of aquatic plant communities by cluster analysis

Numerical classification methods can simulate strategies of intuitive classifications. This paper considers two different intuitive syntaxonomic schemes suggested for stagnant eutrophic fresh-water communities with a view to identifying which among the commonest numerical methods of classification fits the two intuitive schemes best. Comparison of classifications using an information function and discriminant analysis revealed that the different numerical methods simulate different intuitive schemes, but the results of the numerical classifications are always judged superior. Two new syntaxonomic schemes optimizing the sharpness between the syntaxa are proposed.     

Classifications for cesarean section: a systematic review

Background

Rising cesarean section (CS) rates are a major public health concern and cause worldwide debates. To propose and implement effective measures to reduce or increase CS rates where necessary requires an appropriate classification. Despite several existing CS classifications, there has not yet been a systematic review of these. This study aimed to 1) identify the main CS classifications used worldwide, 2) analyze advantages and deficiencies of each system.

Methods and Findings

Three electronic databases were searched for classifications published 1968–2008. Two reviewers independently assessed classifications using a form created based on items rated as important by international experts. Seven domains (ease, clarity, mutually exclusive categories, totally inclusive classification, prospective identification of categories, reproducibility, implementability) were assessed and graded. Classifications were tested in 12 hypothetical clinical case-scenarios. From a total of 2948 citations, 60 were selected for full-text evaluation and 27 classifications identified. Indications classifications present important limitations and their overall score ranged from 2–9 (maximum grade = 14). Degree of urgency classifications also had several drawbacks (overall scores 6–9). Woman-based classifications performed best (scores 5–14). Other types of classifications require data not routinely collected and may not be relevant in all settings (scores 3–8).

Conclusions

This review and critical appraisal of CS classifications is a methodologically sound contribution to establish the basis for the appropriate monitoring and rational use of CS. Results suggest that women-based classifications in general, and Robson''s classification, in particular, would be in the best position to fulfill current international and local needs and that efforts to develop an internationally applicable CS classification would be most appropriately placed in building upon this classification. The use of a single CS classification will facilitate auditing, analyzing and comparing CS rates across different settings and help to create and implement effective strategies specifically targeted to optimize CS rates where necessary.     

The proximate/ultimate distinction in the multiple careers of Ernst Mayr

Ernst Mayr's distinction between “ultimate” and “proximate” causes is justly considered a major contribution to philosophy of biology. But how did Mayr come to this “philosophical” distinction, and what role did it play in his earlier “scientific” work? I address these issues by dividing Mayr's work into three careers or phases: 1) Mayr the naturalist/researcher, 2) Mayr the representative of and spokesman for evolutionary biology and systematics, and more recently 3) Mayr the historian and philosopher of biology. If we want to understand the role of the proximate/ultimate distinction in Mayr's more recent career as a philosopher and historian, then it helps to consider hisearlier use of the distinction, in the course of his research, and in his promotion of the professions of evolutionary biology and systematics. I believe that this approach would also shed light on some other important “philosophical” positions that Mayr has defended, including the distinction between “essentialism: and “population thinking.”     

Using geometric and non‐geometric internal evaluators to compare eight vegetation classification methods

Questions: How similar are solutions of eight commonly used vegetation classification methods? Which classification methods are most effective according to classification validity evaluators? How do evaluators with different optimality criteria differ in their assessments of classification efficacy? In particular, do evaluators which use geometric criteria (e.g. cluster compactness) and non‐geometric evaluators (which rely on diagnostic species) offer similar classification evaluations? Methods: We analysed classifications of two vegetation data‐sets produced by eight classification methods. Classification solutions were assessed with five geometric and four non‐geometric internal evaluators. We formally introduce three new evaluators: PARTANA, an intuitive variation on evaluators which use the ratio of within/between cluster dissimilarity as the optimality criterion, an adaptation of Morisita's index of niche overlap, and ISAMIC, an algorithm which measures the degree to which species are either always present or always absent within clusters. Results and Conclusions: 1. With the exception of single linkage hierarchical clustering, classifications resulting from the eight methods were often similar. 2. Although evaluators varied in their assessment of best overall classification method, they generally favored three hierarchical agglomerative clustering strategies: flexible beta (β=– 0.25), average linkage, and Ward's linkage. 3. Among introduced evaluators PARTANA appears to be an effective geometric strategy which provides assessments similar to C‐index and Gamma evaluators. Non‐geometric evaluators ISAMIC and Morisita's index demonstrate a strong bias for single linkage solutions. 4. Because non‐geometric criteria are of interest to phytosociologists there is a strong need for their continued development for use with vegetation classifications.     

On concept formation in systematics

In his “Grundzüge einer Theorie der phylogenetischen Systematik”, Hennig (1950 ) cited three philosophers: the leading empiricist Rudolf Carnap, the conventionalist Hugo Dingler, and the somewhat more obscure empiricist Theodor Ziehen. David Hull characterized Hennig's “Grundzüge” as one long argument against idealistic morphology. It will here be argued that Hennig attacked idealistic morphology (synonymous with “systematic” morphology) for its mode of concept formation. Building on Carnap and Ziehen, who both looked back on Ernst Cassirer, Hennig argued that the “generic”, “thing” or “class” concept of traditional nomothetic science must be replaced with Cassirer's “relation concept.” According to Hennig, such “emancipation” of systematics from the Aristotelian “species” concept would also allow transcendence from the distinction of idiographic from nomothetic sciences, thus preserving the unity of science. However, the establishment of relations in the construction of a system of order presupposes entities that can be, or are, related. Relations presuppose relata, which in modern systematics are best conceptualized (at least at the supraspecific level) not as Aristotelian classes, nor as individuals as was argued by Hennig and Ziehen, but as tokens of natural kinds. © The Willi Hennig Society 2006.     

The jazz of cladistics*

In this metaphorical ‘composition’, I comment on nine ‘dissonant chords’ related to the drowning out of cladistic performance: (1) DNA-based phylogenetic hypotheses supported only by bootstrap values and without molecular synapomorphies; (2) the use of molecular data to the exclusion of morphological data, with the classification of clades diagnosed by morphological plesiomorphies plus bootstrap values; (3) neglect of the results of the congruence test and how they are interpreted; (4) the combination of character optimization using both model-based and parsimony methods, and its consequences; (5) the need to effectively integrate ontogeny and phylogeny; (6) the estimation of the ages of clades based on molecular-clock analyses; (7) the belief that new methods, theories, and hypotheses are more reliable than old ones, with the idea that model-based analyses achieve better results than parsimony analyses; (8) the false assumption of the irrelevance of classification; and (9) clashes amongst cladists themselves, who endorse distinct methods, philosophies, and theories. Finally, I present 10 ‘refrains’ in order to intensify the cladistic performance.