Taxic homology and three-taxon statement analysis

Three-taxon statement analysis (3TA) and standard cladistic analysis (SCA) were evaluated relative to propositions of taxic homology. There are definite distinctions between complement relation homologs and paired homologs. The complement relation is discussed, relative to rooting, parsimony, and taxic propositions of homology. The complement relation, as implemented in SCA, makes sense only because SCA is a simple evolutionary model of character-state transformation. 3TA is a method for implementing complement relation data from a taxic perspective. The standard approach to cladistic analysis distinguishes taxa by rooting a tree, which means that that approach is incompatible with taxic propositions of homology, because a taxic homology is a hypothesis of relationship between taxa that possess a homolog relative to taxa that lack a homolog. It is not necessary to treat paired homologs from a transformational perspective to distinguish informative from uninformative data. 3TA yields results markedly different from those of SCA. SCA, which seeks to minimize tree length, may not maximize the relation of homology (congruence) relative to a tree.     

THREE-TAXON STATEMENTS AND PHYLOGENY CONSTRUCTION

Abstract — The differences between the three-taxon statement analysis and the standard approach are in the way they explicitly or implicitly consider character homology and modes of character evolution. The differences in the two methods have implications relative to the general model of evolution viewed as descent with modification of characters.     

Transformationalism,taxism, and developmental biology in systematics

Issues concerning transformational and taxic comparisons are central to understanding the impact of the recent proliferation of molecular developmental data on evolutionary biology. More importantly, an understanding of taxism and transformationalism in comparative biology is critical to assessing the impact of the recent developmental data on systematic theory and practice. We examine the philosophical and practical aspects of the transformational approach and the relevance of this approach to recent molecular-based developmental data. We also examine the theoretical basis of the taxic approach to molecular developmental data and suggest that developmental data are perfectly amenable to the taxic approach. Two recent examples from the molecular developmental biology literature--the evolution of insect wings and the evolution of dorsal ventral inversion in vertebrates and invertebrates--are used to compare the taxic and transformational approaches. We conclude that the transformational approach is entirely appropriate for ontogenetic studies and furthermore can serve as an excellent source of hypotheses about the evolution of characters. However, the taxic approach is the ultimate arbiter of these hypotheses.     

On the Three-Taxon Approach to Parsimony Analysis

The following three basic defects for which three-taxon analysis has been rejected as a method for biological systematics are reviewed: (1) character evolution is a priori assumed to be irreversible; (2) basic statements that are not logically independent are treated as if they are; (3) three-taxon statements that are considered as independent support for a given tree may be mutually exclusive on that tree. It is argued that these criticisms only relate to the particular way the three-taxon approach was originally implemented. Four-taxon analysis, an alternative implementation that circumvents these problems, is derived. Four-taxon analysis is identical to standard parsimony analysis except for an unnatural restriction on the maximum amount of homoplasy that may be concentrated in a single character state. This restriction follows directly from the basic tenet of the three-taxon approach, that character state distributions should be decomposed into basic statements that are, in themselves, still informative with respect to relationships. A reconsideration of what constitutes an elementary relevant statement in systematics leads to a reformulation of standard parsimony as two-taxon analysis and to a rejection of four-taxon analysis as a method for biological systematics.     

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.     

ONTOGENY AND THE HIERARCHY OF TYPES

Abstract— The long history of belief in a parallelism between ontogeny and a hierarchical order of natural things is reviewed. The meaning of von Baerian recapitulation is analyzed and its implications for cladistic methodology are discussed at two levels: ontogeny and homology. The basic problem inherent in the purported parallelism is that the order of natural things (i.e., the taxic approach to homology) is part of the "world of being" of Platonic ideas, whereas ontogeny and phylogeny (i.e., the transformational approach to homology) belong to Plato's "world of becoming." These two "genera of existence," as Plato put it, being and becoming, are incompatible but complementary views of nature.     

Contemporary concepts of homology in biology (a theoretical review)

A brief review of the contemporary theoretical concepts of homology being developed basically in systematics and phylogenetics as well as in developmental biology is presented. Ontologically, both homology and analogy represent a kind of correspondence considered from the standpoint of nominalism, realism, and conceptualism. According to their nominalistic treatment, both are described by a set-theory approximation which makes them classes (in the logical sense). The realistic treatment provides their holistic view according to which a homologue is an anatomical or evolutionary singular while analogue remains a class. The conceptualistic treatment means that there are real (objective) correspondences existing among real (objective) entities while fixation of any of them is based on certain theoretical presumptions adopted by a researcher; homology as a natural kind (including homeostatic property cluster) seems to be most consistent with such a treatment. Realistic view of homology makes it "absolute", while two others make discrimination of homology and analogy strictly relative. Two basic general homology concepts have been developed in recent literature--taxic and transformational ones; the first considers respective correspondences as structure relations, the second as process relations. The taxic homology is nearly the same as classical typological one (Owen), while transformational homology unites all its phylogenetic, ontogenetic (developmental) and transformation-typological definitions. Process-structuralistic approach seems to unite both taxic and transformational ones. The latter makes it possible to apply general homology concept not only to structures but to processes as well. It is stressed that homology is not identical to the similarity, the latter being just the means for revealing the former. Some closer consideration is given to phylogenetic, ontogenetic and genetic treatments of homology; significant uncertainty is shown to exist between them which causes the "homology problem". Epistemologically, any homology statement has a status of hypothesis which makes such a statement theory-dependent according to the hypothetic-deductive argumentation scheme. This dependence allows to stress once more the relative nature of homology and analogy correspondences. Some questions concerning operational concepts and criteria of homology are considered. A hierarchical concept of homology seems to be the most promising prospect of future development of the "homology problem".     

Cycles

Intended to support three-taxon analysis (3ta), the proposal that all character states be regarded as terminal would instead undercut that method. The same is true of the idea that cladistic methods should not account for plesiomorphies. Parsimony does not correspond to interpretation 1 for incompletely resolved cladograms. The main argument common to Nelson's (1996) and Nelson and Platnick's (1991) advocacy of three-taxon analysis rests on presupposing its conclusion. While suggesting that parsimony rests on an inferior evolutionary model, Nelson (1996) neither offered nor provided evidence for any alternative. 3ta sometimes favors reversal over parallelism, but in other cases may disregard reversed characters, so that the method seems to lack any coherent theoretical basis.     

Circularity and Independence in Phylogenetic Tests of Ecological Hypotheses

It has been asserted that in order to avoid circularity in phylogenetic tests of ecological hypotheses, one must exclude from the cladistic analysis any characters that might be correlated with that hypothesis. The argument assumes that selective correlation leads to lack of independence among characters and may thus bias the analysis. This argument conflates the idea of independence between the ecological hypothesis and the phylogeny with independence among characters used to construct the tree. We argue that adaptation or selection does not necessarily result in the non-independence of characters, and that characters for a cladistic analysis should be evaluated as homology statements rather than functional ones. As with any partitioning of data, character exclusion may lead to weaker phylogenetic hypotheses, and the practice of mapping characters onto a tree, rather than including them in the analysis, should be avoided. Examples from pollination biology are used to illustrate some of the theoretical and practical problems inherent in character exclusion.     

Taxic Homology = Overall Similarity

Modified three-taxon analysis (m3ta), a method in which three-taxon statements are produced from a nonadditive binary coding of the original data, has been proposed as a model-free way of assessing monophyly of groups, utilizing the taxic concept of homology. In fact the taxic concept amounts to a model, and, further, one that seems to conflict directly with evolution. M3ta is a type of grouping by all similarities and, like all such methods, would require a clock assumption if the tree were to be interpreted phylogenetically. Groupings based on this method, consequently, are phenetic, and they have little to do with monophyly. It has been proposed to define phylogenetic systematics in terms of grouping only by presences. While popular among advocates of 3ta, such definitions are completely inadequate, both because absences may be apomorphic and because phenetic methods can disagree with phylogenetic ones even when no absences are involved.     

THREE STEPS OF HOMOLOGY ASSESSMENT

Abstract — In 1991 de Pinna (Cladistics 7: 367–394) coined the term primary homology as the putative homology statements prior to tree reconstruction. However, some confusion still exists regarding the conjectural nature of homology and to the analysis of DNA sequences. By dividing de Pinna's term primary homology into topographical identity and character state identity, we emphasize the sequential refinement of putative homology statements. We discuss the problem of transformational versus taxic homology and explain the application of our terms to DNA sequence data.     

Homology, biogeography and areas of endemism

Hypotheses of biogeographic homology constitute the basis of historical biogeography. Primary biogeographic homology refers to a conjecture on a common biogeographic history, and secondary biogeographic homology refers to the cladistic test of the formerly recognized homology. Panbiogeography deals with the former, through the recognition of generalized tracks and areas of endemism, whereas cladistic biogeography deals with the latter, through the generation of general area cladograms. A historical biogeographic analysis may include both approaches, in a two‐stage analysis.     

The notion of homology in current comparative biology

Current notions on homology, and its recognition, causation, and explanation are reviewed in this report. The focus is primarily on concepts because the formulation of precise definitions of homology has contributed little to our understanding of the issue. Different aspects or concepts of homology have been contrasted, currently the most important ones being the distinction between systematic and biological concepts. The systematic concept of homology focuses on common ancestry and on taxa; the biological concept tries to explain patterns of conservatism in evolution by shared developmental constraints. Similarity or correspondence is generally accepted as a primary criterion in the delimitation of homologues, albeit that this criterion is not without practical and theoretical problems. Apart from similarity, the biological concept of homology also stresses developmental individuality of putative homologous structures. Structural and positional aspects of homology can be separated, with positional homology acquiring an independent status. Similarity, topographic relationships, and ontogenetic development cannot be tests of homology. Within the cladistic paradigm, the most decisive test of homology is that of congruence; proponents of the biological-homology concept have been less concerned with test implications. Adopting a hierarchical view of nature suggests that characters have to be homologized at their appropriate level of organization. A taxic or systematic approach to homology has precedence over a transformational or biological approach. Nevertheless, pattern analysis and process explanations are not independent of each other.     

Homoplasy, character function, and nemertean systematics

We question recent claims that cladistic analysis is inapplicable in nemerteans (phylum Nemertea) due to a supposedly high degree of convergence. We further argue that terms like convergence and parallelism are historical sayings and only make sense in a phylogenetic context. Therefore, an approach aiming to produce phylogenetic hypotheses cannot be rejected on the grounds of a high degree of convergence before the actual hypothesis. Convergence is not an empirical observation, but a conclusion made after an analysis. We also discuss the view that knowledge of a character's function is a prerequisite for phylogenetic analysis and conclude that this is an invalid approach. Function, like any other way of sharpening our observations, helps in formulating non-phylogenetic hypotheses of homology, but the crucial test is congruence with other characters on a phylogeny.     

Homologies in phylogenetic analyses—concept and tests

Analyzing morphological characters in a phylogenetic context comprises two steps, character analysis and cladistic analysis, which are equivalent to two independent tests for hypotheses on homology. The concept of homology concerns comparable parts of the same or different organisms if their correspondences are the consequence of the same genetic or epigenetic information, and consequently of the same origin. The concept of homology is more inclusive than the character concept. Characters are seen as parts of transformation series. In the first step of morphological character analyses correspondences and non-correspondences between two characters are analyzed. A range of different examination methods and accurate study contribute to the severity of test. The hypothesis that two characters are homologous is corroborated if the correspondences outweigh the non-correspondences because the non-correspondences contradict the homology hypothesis whereas the correspondences contradict the analogy hypothesis. Complex characters possess a higher empirical content than less complex characters because they are more severely testable. The cladistic analysis tests characters against other characters which have all passed the first test. Characters which are congruent with the most parsimonious topology are further corroborated; incongruent characters are not seen as ‘falsified’ but as not further corroborated and subject to re-analysis. To test both homologies and topologies repeatedly is consistent with Popperian testability, and it is in such cycles of research that hypotheses will be critically re-evaluated.     

A Reconsideration of the Coding of Inapplicable Characters: Assumptions and Problems

Character coding entails assumptions that may be problematic within the context of parsimony analysis using current computer algorithms. The example discussed here involves a character-variable (e.g., tail color) that is inapplicable in some taxa in the analysis because the part (e.g., tail) with which it is associated is lacking in those taxa. The part and character-variable can be coded as separate characters, or they can be fused into a single character. If the part and character-variable are coded as separate characters there is transformational independence between the part and the character-variable, but the logical dependence inherent to the hierarchical relationship between the part and its character-variable is only partly accounted for. Fusing the part and character-variable into one multistate character fully accounts for the logical dependence, but it is equivocal regarding the transformational independence. Separate coding is consistent with the primary homology statement that the part is homologous in all taxa possessing it, whereas fused coding is equivocal regarding this hypothesis of primary homology. As a result fused coding involves a loss of phylogenetic information. Use of a stepmatrix or other mechanisms associated with fused coding that preserve this phylogenetic information involves weighting schemes or ordered characters that have other assumptions that may also be difficult to justify.     

When molecules and morphology clash: reconciling conflicting phylogenies of the Metazoa by considering secondary character loss

Molecular and morphological data sets have yielded conflicting phylogenies for the Metazoa. So far, no general explanation for the existence of this conflict has been suggested. However, I believe that a neglected aspect of metazoan cladistics has introduced a systematic and substantial bias into morphological phylogenetic analyses. Most characters used for metazoan cladistics are coded as binary absence/presence characters. For most of these characters, the absence states are assumed to be uninformative default plesiomorphies, if they are defined at all. This character coding strategy could seriously underestimate the number of informative apomorphic absences or secondary character losses. Because nodes in morphological metazoan phylogenies are typically supported by relatively small numbers of characters each with a potentially strong impact on tree topology, failure to distinguish between primary absence and secondary loss of characters before a cladistic analysis may mislead morphological cladistics. This may falsely suggest conflict with molecular phylogenies, which are not sensitive to this bias. To test the existence of this bias, I compare the phylogenetic placement of a variety of metazoan taxa in molecular and morphological trees. In all instances investigated here, phylogenetic conflict can be resolved by allowing for secondary loss of morphological characters, which were assumed to be primitively absent in cladistic analyses. These findings suggest that we should be cautious in interpreting the results of morphological metazoan cladistic analyses and additionally illustrate the value of a more functional approach to comparative morphology in certain circumstances.     

Using genetic networks and homology to understand the evolution of phenotypic traits

Homology can have different meanings for different kinds of biologists. A phylogenetic view holds that homology, defined by common ancestry, is rigorously identified through phylogenetic analysis. Such homologies are taxic homologies (=synapomorphies). A second interpretation, "biological homology" emphasizes common ancestry through the continuity of genetic information underlying phenotypic traits, and is favored by some developmental geneticists. A third kind of homology, deep homology, was recently defined as "the sharing of the genetic regulatory apparatus used to build morphologically and phylogenetically disparate features." Here we explain the commonality among these three versions of homology. We argue that biological homology, as evidenced by a conserved gene regulatory network giving a trait its "essential identity" (a Character Identity Network or "ChIN") must also be a taxic homology. In cases where a phenotypic trait has been modified over the course of evolution such that homology (taxic) is obscured (e.g. jaws are modified gill arches), a shared underlying ChIN provides evidence of this transformation. Deep homologies, where molecular and cellular components of a phenotypic trait precede the trait itself (are phylogenetically deep relative to the trait), are also taxic homologies, undisguised. Deep homologies inspire particular interest for understanding the evolutionary assembly of phenotypic traits. Mapping these deeply homologous building blocks on a phylogeny reveals the sequential steps leading to the origin of phenotypic novelties. Finally, we discuss how new genomic technologies will revolutionize the comparative genomic study of non-model organisms in a phylogenetic context, necessary to understand the evolution of phenotypic traits.