Literal transformation is in the realtime of an individual organism only, its entire ontogeny; it is not what is meant by evolutionary transformation. "Universals" having to do with development, even the immensely deep homologies (orthologies) of hox-genes, are contingency bound. They are therefore subject to historical understanding, not just to rules that consider some developmental attributes universal, or to the methodology of parsimony algorithms. Darwinian phylogenetic analysis is a historical narrative method to attain contingency-based explanations, and it represents the combination of several research programs, not just morphological approaches. Darwinian phylogenetics addresses the issues of contingency and adaptation that cannot be isolated from one another when we seek to understand phylogenetic transformations of attributes and lineage reconstructions.

Spatio-temporal and functional factors surrounding morphology provide the grist for the mill of phyletics in character analysis. Both the phyletics and cladistics of taxa depend on these. Rapid advances in developmental genetics, the understanding of modularity in the developing organism, and a concerted use of functional and ecological biology, together with a fossil record, can play a critical part in this approach that has to be tailored both to the groups analyzed and the levels at which it is employed. However, "ultrafunctionalist" perspectives on adaptations (e.g., some gene-selectionist, sociobiological, explanations) , in which cost-benefit evaluations and a lack of historical perspective dominate, are not concordant with Darwin's own history-guided understanding of adaptive evolution.

Transformational analysis, whether based solely or partly on the sequences offered by the fossil record, and morphological analysis based on functional-adaptive foundations are the cornerstones of phylogenetic analysis. Any and all theoretically meaningful contextual determinations of which trait is primitive and which is advanced involves some type of transformational assessment and should use a geographical and stratigraphical perspective when these are feasible. Sometimes very convincing stratigraphical distributions of abundant data dramatically demonstrate how attempts to shoehorn such evidence into the prescriptions of cladistic analysis distort a phylogeny when segments of lineages are forced into "terminal" species taxa to conform to cladistic practice. This was dramatically and painstakingly demonstrated by Redline (1997) in his rigorous stratigraphically controlled study of the largely Wasatchian (North American early Eocene) small mammal, the condylarth Hyopsodus. Such information (and astute analysis) is often rare at the population or taxonomic species levels, but the context of biostratigraphical information is critical, even if problems and analysis are at a higher level, removed from species taxa.

Beyond the best estimate of phylogenetic topology for the groups of organisms studied, an important goal of taxonomy (in keeping with Darwinian aims) is to strive for properly demarcated, monophyletic taxa diagnosed by apomorphies of their stems with the clear understanding that the base delineation must depend on both the availability of information and some heuristically meaningful sense. The unsuitability of the Linnean system for evolutionary depictions, created at a time when non-evolutionary and atemporal sorting was the aim of taxonomy, has been often discussed in spite of its suitability for punctuationism and taxogram views of evolution. The continuity of evolutionary lineages and the inability of the Linnean system to deal with time make taxic analysis of phylogeny flawed from its very inception (but for some recurrent suggestions for fossils see Redline (1997)). In taxic analysis, taxa are considered the starting point for both the phylogeny of the taxa themselves and, subsequently, for the understanding the polarity of traits. This is a fundamental tenet of most parsimony-based cladistics. Nearly invariably, these views are tied to an ontological conception of species (which are in reality species taxa) through time. Ontologically a species in a moment of time is a segment of its lineage, and only extant representatives are unequivocally terminal, although undoubtedly millions of lineages became extinct. Nevertheless, those practicing taxic analysis base their ideas of a species taxon on the conception that species, and other taxa are "individuals". These same systematists also often oppose the transformational analysis of taxonomic properties in systematics and argue for the decoupling of phylogenetic analysis from evolutionary theory (e.g., Rieppel 1993). The result is an advocacy of methods based on a structuralist theory of evolutionary transformation that is wedded to and derived from the practical procedures of delineating species and other taxa. Such efforts invariably yield theories that selectively mix the conceptual foundations of tested evolutionary dynamics with epistemic criteria and notions derived from the latter. Consequently, such theories are simply epistemic, without ontological foundations and provide inadequate conceptual methods for character analysis.

Systematists who reject transformational analysis also usually adhere to the notion that there is something causally and processually distinct in the origin of a new lineage (speciation) and its perseverance from anagenetic (= phyletic) evolutionary change itself. They realize that transformational analysis poses a core disagreement with the tenets of hierarchic punctuationism, a fundamentally taxic (and speciational) view of evolution. Yet such a disagreement is minor. The conceptual step needed to acknowledge is that the real history of lineage continuity and splitting appears jagged due to extinction and the missing fossils of the variably evolving lineages. Only unwarranted assumptions about species (lineages) and the artificial gaps in the fossil record permit a fully taxic view of the evolutionary process. Punctuationists and cladism-based taxonomic theorists have had a long history of sidestepping the issue of transformation, but their real problem is with the concept of anagenetic change in lineages. Anagenetic transformation is an obvious impediment for those who want to have a causal macroevolutionary evolutionary theory in which taxa, the "individuals," do the evolving. Populations and species evolve, lineages are their record, and there are no theoretically meaningful boundaries in time-successive realtime populations/species to satisfy taxonomic conventions. Delineations of time-successive species taxa are necessary, but they do not, by themselves, inform about the nature of the evolutionary process itself in undivided lineages. As a result of this theoretical conflict, an expanding Synthesis stands in the way of taxic and hierarchic punctuationists who want to weave another evolutionary theory from taxic operationalism (Szalay 1999a).

Linked attacks on the phenomenon of mosaic evolution, a genuine pattern description, as a "hoary old concept" in order to drive arguments against the straw man of transformationism in systematics are unfortunate. Such views are particularly surprising in light of the increasing evidence from developmental biology that modularity (and the often striking independence of the modules within the same organism) is very probable. It is a mistake to believe that natural selection cannot favor individuals that retain some attributes that continue to interact with selection in an unchanged manner while these same individuals have new characters that fulfill other aspects of their adaptedness. Any argument against the phenomenon of mosaic evolution not only betrays too much reliance on outdated concepts of epistasis, but it also misses fundamentally pattern-based observations about taxa.

Adherents of parsimony-based cladistics or punctuationism, whether they are against transformational analysis or against the observationally- based concept of mosaic evolution, often inadvertently reject some of the great advances of both Darwinian evolutionism and the Modern Synthesis, yet they also strive at the same time to accommodate the centrality of adaptation. The facts that functionally and adaptively highly-correlated attributes of one character complex may have remained stagnant (e.g., due to stabilizing selection), whereas others have evolved in various directions (even in populations of the same species), attest to the differential adaptedness of different lineages. Students of speciose groups of vertebrates know well that, although some attributes are species-specific, other complexes can remain virtually identical at higher taxonomic levels. It has been repeatedly corroborated that aspects of taxa evolve at different rates (Simpson 1953). It has also been noted that often chronologically older adaptations contain the structural and functional limits needed for new behaviors, and therefore these older complexes do not evolve significantly for long periods of time. Equally prevalent are some well-established structural adaptations that simply channel the relevant functions associated with newer roles.

As examples of mosaic patterns, the attainment of functionally well-honed stages in the metapodials (as well as the carpals and tarsals) of different genera of perissodactyls, artiodactyls, or the universal modification of the first phalanx of the first ray of the foot of all bats to be approximately 1.5 times longer than the equivalent units lateral to it (probably for an ancestral tail-hook landing technique connected with the attainment of flight; see Szalay and Lucas 1993) did not prevent a riot of cranial and dental, and a plethora of other, evolutionary differentiation within these groups. How could we contemplate the recovery of phylogeny if it were not for the persistence of homologous similarities of varying antiquity? Highly and causally- corroborated correlations of homologies and synapomorphies in different lineages attest to the fact that the phenomenon of mosaic evolution is a cornerstone of an independent transformational analysis of traits, in contradistinction to taxon-driven, and most often parsimony-driven, "transformational" analysis. Whatever the rate of evolution of such events, hundreds of examples may be cited from the patterns of vertebrate taxic diversity. Even episodic changes are gradual because gradualism in the Darwinian sense is rate-independent (see Simpson 1953).

Taxonomy reflects the painstaking and only partially recovered evidence of evolving lineages and their diversity at any time. It is a result of efforts to construct meaningful taxonomic species and somehow express their relationships in higher monophyletic taxa in order to gauge organic diversity and to provide the necessary heuristics for the study of the history of life. Fossil-species taxa are not reliable equivalents of modern species, which can be delineated by their reproductive discontinuity in contrast to other species. They are certainly not all "terminal taxa." Rather, fossil species are estimates devised by trained taxonomists, and based on selected models of extant species that have been well studied regarding their geographical distributions, attributes, and sometimes genetics, as well as the various forms of intergradations of their populations (Jolly 1993; Szalay 1993; various papers in Kimbel and Martin 1993). These fossil species taxa are certainly not all new lineages but many undoubtedly represent lineage segments, as all taxonomic species do. This notion of taxonomic species also applies to living-species taxa that often incorporate samples of precedent populations of varying antiquity.