Homology and errors

A recent review of the homology concept in cladistics is critiqued in light of the historical literature. Homology as a notion relevant to the recognition of clades remains equivalent to synapomorphy. Some symplesiomorphies are “homologies” inasmuch as they represent synapomorphies of more inclusive taxa; others are complementary character states that do not imply any shared evolutionary history among the taxa that exhibit the state. Undirected character‐state change (as characters optimized on an unrooted tree) is a necessary but not sufficient test of homology, because the addition of a root may alter parsimonious reconstructions. Primary and secondary homology are defended as realistic representations of discovery procedures in comparative biology, recognizable even in Direct Optimization. The epistemological relationship between homology as evidence and common ancestry as explanation is again emphasized. An alternative definition of homology is proposed. © The Willi Hennig Society 2012.     

Nachtrag zu ‘Hepaticae Bomeenses (Oxford University Expedition to Sarawak, 1932)’

Abstract

Recent empirical advances in bryophyte systematics have been made in the discovery and detailed study of new characters. However, theoretical considerations have not kept pace. Proper attention has not been paid to how these new characters can be used to discover relationships among groups and produce classifications. Recent cladistic studies of the relationships of the major groups of bryophytes have demonstrated the feasibility and usefulness of an approach to phylogenetic systematics derived from the works of Hennig. A Hennigian approach attempts to find the particular hierarchical level at which a given character is a homology (i.e. a synapomorphy or shared, derived character), relationships are established by searching for congruent patterns of homologies, and the resulting hierarchical scheme is used as the basis for a classification. Such an approach provides a rigorous and explicit logic for investigating phylogeny and recognizing natural, historically discrete taxa. The theoretical advantages of a Hennigian approach are discussed and illustrated by examining the congruence of new characters data with preliminary cladograms of the major bryophyte groups.     

On homology

Homology in cladistics is reviewed. The definition of important terms is explicated in historical context. Homology is not synonymous with synapomorphy: it includes symplesiomorphy, and Hennig clearly included both plesiomorphy and synapomorphy as types of homology. Homoplasy is error, in coding, and is analogous to residual error in simple regression. If parallelism and convergence are to be distinguished, homoplasy would be evidence of the former and analogy evidence of the latter. We discuss whether there is a difference between molecular homology and morphological homology, character state homology, nested homology (additive characters), and serial homology. We conclude by proposing a global definition of homology. ©The Will Henning Society 2011.     

Homology assessment in parsimony and model‐based analyses: two sides of the same coin

The present paper is mainly concerned with homology assessment through phylogenetic analyses. It raises a fundamental question: What are the epistemological differences between modern parsimony and model‐based analyses in relation to homology assessment and phylogenetic inference? Although these methods usually achieve concordant topological results, they may generate discordant inferences of character evolution from the same datasets. This indicates that method selection has serious implications for evolutionary scenarios and classificatory arrangements. Notwithstanding that parsimony and model‐based approaches use the Hennigian concepts of monophyly and synapomorphy, they employ different epistemological ways of dealing with the monophyly/synapomorphy relationship. Independently of their differences, these analyses should take into account all relevant evidence in support of the phylogenetic inferences. A focus on morphological homologues means that they must be included in data matrices, evaluated as part of the phylogenetic analysis, and cannot be ignored in calculation of the tree(s) length (parsimony), maximum‐likelihood (maximum‐likelihood), and posterior probabilities (Bayes).     

Homology and synapomorphy‐symplesiomorphy—neither synonymous nor equivalent but different perspectives on the same phenomenon

In a recent debate, either synapomorphy and symplesiomorphy or only synapomorphy have been claimed to be synonymous or equivalent to homology. In my view, exactly the same relationship exists between homology supported by a congruence test on the one hand and synapomorphy as well as symplesiomorphy on the other hand. Both conditions become established at the same time with the process of rooting of an unrooted topology. I, however, do not consider the concept of homology equal or synonymous to that of synapomorphy and symplesiomorphy. In my view, they represent different perspectives on the same phenomenon, i.e. correspondence by common origin. Homology has no implication on the direction of transformation, whereas symplesiomorphy as “primitive” condition and synapomorphy as “derived” condition refer directly to phylogenesis, the real historical evolutionary process of speciation and transformation. In addition, synapomorphy and symplesiomorphy might also refer to a character state that refers to the absence of a structure/organ, which creates problems with traditional homology concepts. Hennig's terms synapomorphy and symplesiomorphy are necessary and sufficient for the evolutionary interpretation of character states. For what is corroborated in an unrooted topology as the result of a congruence test, I suggest as a new term “synmorphy” because it can well be applied also to those characters where one state represents the absence of a structure/organ. The place for homology in morphological cladistics, however, is restricted to the characterization of the relationship between different character states of one transformation series (i.e. character).     

Transformation Series as an Ideographic Character Concept

An ideographic concept of character is indispensable to phylogenetic inference. Hennig proposed that characters be conceptualized as “transformation series”, a proposal that is firmly grounded in evolutionary theory and consistent with the method of inferring transformation events as evidence of phylogenetic propinquity. Nevertheless, that concept is usually overlooked or rejected in favor of others based on similarity. Here we explicate Hennig's definition of character as an ideographic concept in the science of phylogenetic systematics. As transformation series, characters are historical individuals akin to species and clades. As such, the related concept of homology refers to a historical identity relation and is not equivalent to or synonymous with synapomorphy. The distinction between primary and secondary homology is dismissed on the grounds that it conflates the concept of homology with the discovery operations used to detect instances of that concept. Although concern for character dependence is generally valid, it is often misplaced, focusing on functional or developmental correlation (both of which are irrelevant in phylogenetic systematics but may be valid in other fields) instead of the historical/transformational independence relevant to phylogenetic inference. As an ideographic science concerned with concrete objects and events (i.e. individuals), intensionally and extensionally defined properties are inconsistent with the individuation of characters for phylogenetic analysis, the utility of properties being limited to communicating results and facilitating future rounds of testing.     

THE MYTH OF OBJECTIVITY—POST-HENNIGIAN DEVIATIONS

Abstract— The punctuated equilibrium speciation mode is an implied consequence of the deviation rule and the differences between cladograms and phylogenetic trees implicitly were recognized by Hennig. Neocladism and transformed cladism, however, both are contradictory to the view of Hennig. Neither of them will be consistent when parallel changes exceed informative unparallel changes, which in the real world there are many indications to believe they do. In three tables cladogenetic trends used in erecting three schemes of argumentation, on the specific, generic, and subfamily levels respectively, are analyzed and divided into: " objective" synapomorphies not allowing for outside parallelism or secondary change, subjective synapomorphies , and underlying synapomorphies . Evaluations based on the strictest criteria for asserting synapomorphy are possible only when comparing higher taxa of subfamily level and up. On the generic level trends showing outside parallelism can be rejected if all other possibly synapomorphic trends are included. On the specific level it is necessary to take all kinds of synapomorphies into consideration, including those showing outside parallelism. There may often be a preponderance of trends caused by parallel selection in taxa with specialized sexual and/or feeding behaviors, as exemplified by some chironomid male imagines and larvae. It is necessary to have knowledge of the nature of the different possible natural processes and try to explain these before undertaking estimations of patterns of kinship. The persistent intuitive and subjective element in phylogenetics was stressed by Hennig. Objectivity is a myth.     

The taxonomic status of Lithophyllum stìctaeforme (Rhodophyta, Corallinales) and its generic position in light of phylogenetic considerations

The type of Lithophyllum stìctaeforme (Areschoug) Hauck (‵ Melobesia stictaeformis Areschoug in J. Agardh) is re-examined and shown to be conspecific with a common Mediterranean foliose coralline recently recognized as Lithophyllum frondosum (Dufour) Furnari, Cormaci et Alongi (‵ Melobesia frondosa Dufour) and previously known by the misapplied name Lithophyllum (Pseudolithophyllum) expansum Philippi. The generic position of the species in Lithophyllum or Pseudolithophyllum is phylogenetically examined, in the Hennigian sense. It is shown that secondary perithallial outgrowths ('faux hypothalle') may represent a synapomorphy for these genera that traditionally have been segregated from each other by the presence, respectively absence, of a coaxial 'faux hypothalle'. Recognition of both Lithophyllum and Pseudolithophyllum by virtue of a single character in its two states (absent vs. present) is however not tenable, if these genera are considered to be sister-taxa.     

How to Read a Phylogenetic Tree

It has been over 50 years since Willi Hennig proposed a new method for determining genealogical relationships among species, which he called phylogenetic systematics. Many people, however, still approach the method warily, worried that they will have to grapple with an overwhelming number of new terms and concepts. In fact, reading and understanding phylogenetic trees is really not difficult at all. You only need to learn three new words, autapomorphy, synapomorphy, and plesiomorphy. All of the other concepts (e.g., ancestors, monophyletic groups, paraphyletic groups) are familiar ones that were already part of Darwinian evolution before Hennig arrived on the scene.     

A cladistic approach to relationships in pentastomida.

The positioning of the Pentastomida among the Metazoa has provoked many debates up to the present. On the other hand, the internal relationships among the pentastomid subgroups have received much less attention in the past. We provide the first phylogenetic analyses under Hennigian principles. Thirty-two morphological characters were selected from the primary literature, analyzed manually, and then with the program Hennig86. Four most parsimonious trees were obtained; these were analyzed by successive weighting and reduced to 1 consensus cladogram 380 steps long, with a consistency index of 0.98 and a retention index of 0.99. Characters were also analyzed as unordered, producing results that were congruent with the previous analyses. The internal groups were ordered according to the following system: (Heymnonsicambria + Haffnericambria + Backlericambria (Cephalobaenida (Railietiellida nov. (Reighardiida nov. (Porocephalida (Linguatuloidea (Linguatulidae + Subtriquetridae) + Porocephaloidea (Sebekidae + Porocephalidae))))))). This phylogenetic system is largely congruent with the first modern taxonomic arrangement proposed for the Pentastomida.     

The statistical reliability of synapomorphic analyses

A statistical test has been developed to ascertain whether a given number of presumptive synapomorphies between one pair of taxa is significantly greater than the number between another pair of taxa. This is shown to be a form of testing the significance of a difference between two proportions. It is necessary first to adjust for common patterns of synapomorphy that raise or lower both numbers. The method has been checked by simulation, and is illustrated by data on the relationships of tetrapods. It proves that Hennigian cladistics has statistical constraints.     

ON THE BOUNDARIES OF PHYLOGENETIC SYSTEMATICS

Abstract— The parsimony criterion both measures the ability of genealogical hypotheses to explain observed similarities and corresponds to Hennig's principle of grouping by synapomorphy. Sæther's proposal of grouping according to homoiology is neither Hennigian nor justified on any other grounds. Criticisms by Felsenstein that parsimony analysis may be statistically inconsistent lead to an equivalent criticism of all statistical methods, and so are of no value for evaluating phylogenetic methods.     

Heterology: the shadows of a shade

The recent proposition to name some similarities not due to common ancestry as examples of heterology is discussed from a historical point of view. The use of an elaborate terminology for various kinds of similarities is examined and rejected in favor of dealing with homology and non‐homology. © The Willi Hennig Society 2006.     

Midges and the electronic Ouija board The phylogeny of the Hydrobaenus group (Chironomidae, Diptera) revised

Cranston and Humphries (1988) expose Sæther's (1976) revision of the Hydrobaenus grou of enera (Chironomidae, Ditera) to the vagaries of quantitative phyletics. In the rocess they have clearly shown why at feast their method is not in accordance with the view of Hennig. In the qualitative Hennigian method the parsimony criterion is used when choosing among alternative hypotheses of explanation of single character distribution. The selection and interpretation equals the cladogenetic analysis. In neocladistic methods the parsimony criterion is usel in order to find the tree implying the fewest evolutionary ains and losses with the fewest lines. The explanation of characters enters as an afterthought. The differences between the methods are shown by analyzing a theoretical data matrix as well as by reassessment of the results obtained by Cranston and Humphries. Their data critique is met point by oint, their data matrix, which is to a large extent erroneous, is corrected, and their data reanalyzed using their and alternative outgroups. The tree topologies remain similar to each other as well as to the original qualitative analysis since there is little inside homoplasy but the changes proposed by Cranston and Humphries are shown invalid.     

Are monophyly and synapomorphy the same or different? Revisiting the role of morphology in phylogenetics

Species are groups of organisms, marked out by reproductive (replicative) properties. Monophyletic taxa are groups of species, marked out by synapomorphies. In Nelson’s analysis, monophyly and synapomorphy are identical relations. Monophyly and synapomorphy, however, are not equivalent relations. Monophyly is epistemically not accessible, whereas synapomorphy is epistemically accessible through character analysis. Monophyly originates with speciation, the two sister‐species that come into being through the splitting of the ancestral species lineage forming a monophyletic taxon at the lowest level of inclusiveness. Synapomorphy provides the empirical evidence for monophyly, inferred from character analysis in the context of a three‐taxon statement. If synapomorphy and monophyly were equivalent, phylogenetic systematists should find a single tree, instead of multiple equally parsimonious trees. Understanding synapomorphy as the relevant evidence for phylogenetic inference reveals a category mistake in contemporary phylogenetics: the treatment of morphological characters mapped onto molecular trees as synapomorphies and homoplasies. The mapping of morphological characters onto nodes of a molecular tree results in an empirically empty procedure for synapomorphy discovery. Morphological synapomorphies and homoplasies can only be discovered by morphological and combined analyses. The use of morphology in phylogenetic inference in general is defended by examples from Laurales and Squamata in particular. To make empirical evidence scientifically relevant in order to search for concordance, or dis‐concordance, of phylogenetic signal, is certainly more fruitful for phylogenetics than the uncritical mapping of morphological traits on a molecular scaffold. © The Willi Hennig Society 2010.     

About nothing

In light of recent terminological controversy, this article reviews cladistic conceptions of character states coded as absences, symplesiomorphies, and secondary losses. The first section addresses absence as a question of ontology vs. epistemology. The second and third sections address the evidentiary status of symplesiomorphy in cladistics, the fourth contrasts primitive absence with secondary loss, and the fifth clarifies the meaning of “grouping”. While secondary losses (reversals) are often synapomorphies, symplesiomorphies (“absent” or otherwise) have no evidentiary import to cladistic hypotheses of relationship. Thus, we argue that identifying symplesiomorphic character states as “homologous” is conceptually vacuous, because they are either synapomorphies (homologues) of more inclusive taxa, or complementary absences that unite no group.     

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.     

Quantitative tests of primary homology

In systematic biology homology hypotheses are typically based on points of similarity and tested using congruence, of which the two stages have come to be distinguished as “primary” versus “secondary” homology. Primary homology is often regarded as prior to logical test, being a kind of background assumption or prior knowledge. Similarity can, however, be tested by more detailed studies that corroborate or weaken previous homology hypotheses before the test of congruence is applied. Indeed testing similarity is the only way to test the homology of characters, as congruence only tests their states. Traditional homology criteria include topology, special similarity, function, ontogeny and step‐counting (for example, transformation in one step versus two via loss and gain). Here we present a method to compare quantitatively the ability of such criteria, and competing homology schema, to explain morphological observations. We apply the method to a classic and difficult problem in the homology of male spider genital sclerites. For this test case topology performed better than special similarity or function. Primary homologies founded on topology resulted in hypotheses that were globally more parsimonious than those based on other criteria, and therefore yielded a more coherent and congruent nomenclature of palpal sclerites in theridiid spiders than prior attempts. Finally, we question whether primary homology should be insulated as “prior knowledge” from the usual issues and demands that quantitative phylogenetic analyses pose, such as weighting and global versus local optima. © The Willi Hennig Society 2007.     

Grundsätze der phylogenetischen Systematik (Eine praxisorientierte Übersicht)

The essential elements of phylogenetic systematics in the sense of Hennig are emphasized: The search for synapomorphies based on a special method of comparative morphology, and the aim of an exclusive use of synapomorphies for kinship proof and the basis of systematics. Special aspects of comparative morphology are: “Directed comparisons” steady reciprocal reflection between comparative morphological result and the system methodical efforts for the realization of distinctive details, comprehensive documentation and functional interpretation. This is equally true for recent and fossil forms. Most suitable for the method (in the sense defined above) are groups with numerous differentiated morphological characters, which can also be preserved in the fossil state. The less this is the case the less is the chance for achieving necessary numbers of well proven synapomorphies. Even so, it is not permitted—for those who want to perform phylogenetic systematics in the sense of Hennig—to use convergences, parallelisms or symplesiomorphies in the sense of “synapomorphies” as phylogenetic arguments for kinship relations. Numerous examples and diagrams demonstrate the methodological proceeding, and differences towards other methods of phylogenetical reconstruction and interpretation. Special attention is paid to direct and indirect conclusions drawn from fossils: Time of origin of characters, stem groups and *groups; predictions concerning the appearance (set of characters) of fossils and simultaneous existence of “neighbour groups” (sister groups, and more distantly related taxa).