THE RELATIONSHIP BETWEEN EVOLUTIONARY THEORY AND PHYLOGENETIC ANALYSIS

The relationship between phylogenetic reconstruction and evolutionary theory is reassessed. It is argued here that phylogenies, and evolutionary principles, should be analysed initially as independently from each other as possible. Only then can they be used to test one another. If the phylogenies and evolutionary principles are totally consistent with one another, this consilience of independent lines of evidence increases confidence in both. If, however, there is a conflict, then one should assess the relative support for each hypothesis, and tentatively accept the more strongly supported one. We review examples where the phylogenetic hypothesis is preferred over the evolutionary principle, and vice versa, and instances where the conflict cannot be readily resolved. Because the analyses of pattern and process must initially be kept separate, the temporal order in which they are performed is unimportant. Therefore, the widespread methodology of always proceeding from cladogram to evolutionary ‘scenario’ cannot be justified philosophically. Such an approach means that cladograms cannot be properly tested against evolutionary principles, and that evolutionary ‘scenarios’ have no independent standing. Instead, we propose the ‘consilience’ approach where phylogenetic and evolutionary hypotheses are formulated independently from each other and then examined for agreement.     

Evolutionary theory and systematics: relationships between process and patterns

The relevance of the Modern Evolutionary Synthesis to the foundations of taxonomy (the construction of groups, both taxa and phyla) is reexamined. The nondimensional biological species concept, and not the multidimensional, taxonomic, species notion which is based on it, represents a culmination of an evolutionary understanding. It demonstrates how established evolutionary mechanisms acting on populations of sexually reproducing organisms provide the testable ontological basis of the species category. We question the ontology and epistemology of the phylogenetic or evolutionary species concept, and find it to be a fundamentally untenable one. We argue that at best, the phylogenetic species is a taxonomic species notion which is not a theoretical concept, and therefore should not serve as foundation for taxonomic theory in general, phylogenetics, and macroevolutionary reconstruction in particular. Although both evolutionary systematists and cladists are phylogeneticists, the reconstruction of the history of life is fundamentally different in these two approaches. We maintain that all method, including taxonomic ones, must fall out of well corroborated theory. In the case of taxonomic methodology the theoretical base must be evolutionary. The axiomatic assumptions that all phena, living and fossil, must be holophyletic taxa (species, and above), resulting from splitting events, and subsequently that evaluation of evolutionary change must be based on a taxic perspective codified by the Hennig ian taxonomic species notion, are not testable premises. We discuss the relationship between some biologically, and therefore taxonomically, significant patterns in nature, and the process dependence of these patterns. Process-free establishment of deductively tested “genealogies” is a contradiction in terms; it is impossible to “recover” phylogenetic patterns without the investment of causal and processual explanations of characters to establish well tested taxonomic properties of these (such as homologies, apomorphies, synapomorphies, or transformation series). Phylogenies of either characters or of taxa are historical-narrative explanations (H-N Es), based on both inductively formulated hypotheses and tested against objective, empirical evidence. We further discuss why construction of a “genealogy”, the alleged framework for “evolutionary reconstruction”, based on a taxic, cladistic outgroup comparison and a posteriori weighting of characters is circular. We define how the procedure called null-group comparison leads to the noncircular testing of the taxonomic properties of characters against which the group phylogenies must be tested. This is the only valid rooting procedure for either character or taxon evolution. While the Hennig -principle is obviously a sound deduction from the theory of descent, cladistic reconstruction of evolutionary history itself lacks a valid methodology for testing transformation hypotheses of both characters and species. We discuss why the paleontological method is part of comparative biology with a critical time dimension ana why we believe that an “ontogenetic method” is not valid. In our view, a merger of exclusive (causal and interactive, but best described as levels of organization) and inclusive (classificatory) hierarchies has not been accomplished by a taxic scheme of evolution advocated by some. Transformational change by its very nature is not classifiable in an inclusive hierarchy, and therefore no classification can fully reflect the causal and interactive chains of events constituting phylogeny, without ignoring and contradicting large areas of corroborated evolutionary theory. Attempts to equate progressive evolutionary change with taxic schemes by Haeckel were fundamentally flawed. His ideas found 19th century expression in a taxic perception of the evolutionary process (“phylogenesis”), a merger of typology, hierarchic and taxic notions of progress, all rooted in an ontogenetic view of phylogeny. The modern schemes of genealogical hierarchies, based on punctuation and a notion of “species” individuality, have yet to demonstrate that they hold promise beyond the Haeckel ian view of progressive evolution.     

A Review on Cladistics

The theoretical bases and approaches of cladistics and some specific problems that, directly or indirectly, rely on cladistic analysis for their revolution, are outlined and discussed. Seven sections comprise this paper: a ) the philosophical foundation of cladistics; b) the theoretical tenets of cladistics; c) the operational procedure of cladisties; d) three schools of classification; e) cladistics and biogeography; f) cladistics and hybrid recognition; and g) is cladistic systematics a scientific theory ? Considerations of scientific methodology involve philosophical questions. From this point, Popper'falsificationism serves a good foundation. Popper emphasizes that all scientific knowledge is hypothetical-deductive, consisting of general statements (theories) that can never be confirmed or verified but only falsified. The theories, that can be tested most effectively, are preferable. Cladistics, aiming at generating accurately expressed and strictly testable systematic hypotheses, is well compatible with this requirement. The principles central to the cladistic theory and methodology are: the Principle of Synapomorphy; the Principle of Strict Monophyly; and the Principle of Strict Parsimony. The first requires forming nested groups by nesting statements about shared evolutionary novelties (synapomorphy) postulated from observed similarities and is the primary one. The second is mainly methodological, subject to modification and compromise. The principle of strict parsimony specifies the most preferable hypothesis (namely the one exhibiting the most congruence in the synapomorphy pattern). The operational procedure that might be followed in formulating and testing hypotheses of the synapomorphy pattern (the cladogram itself) consists of five steps. The erections of monophyletic groups, to a greater or lesser extent, rely on the hypothesis of the previous systematic studies and is the starting point for cladistic analysis. Character analysis, which focuses on character distribution and determination of the polarities, decides the reconstructed phylogeny. A detailed discussion on the methodological principles for identifying transformation sequence is presented. Many algorithms have been designated to infer the cladogram, and are basically of parsimony techniques and Compatibility techiques. The thus yielded cladograms, with their expected pattern of congruent synapomorphies, are tests of a particular hypothesis of synapomorphy and reciprocally synapomorphies are tests of cladistic hypothesis (cladogram). Such reciprocity is a strong stimulus to profound understanding on phylogenetic process and phyletic relationships. The cladogram and the Linnaean classification have the identical logic structure and the set-membership of the two can be made isomorphic. There are three principal approaches to biological classification : cladistics, phenetics and evolutionary classification. Cladistics is the determination of the branching pattern of evolution, and in the context of classification, the development of nested sets based on cladograms. Phenetics is the classification by overall similarities, without regard to evolutionary considerations. Evolutionary classification attempts to consider all meaningful aspects of phylogeny and to use these for making a classification. The last approach has been done intuitively, without explicit methods. An enumeration of their differences and a discussion on their relative merits are presented. Three theoretical approaches have been proposed for interpreting biogeographical history: the phylogenetic theory of biogeography, classical evolutionary biogeography and vicariance biogeography. The former two show some similarities in that they usually look upon biogeography in terms of centers of origin and dispersal from the centers. But the first puts a strong emphasis on the construction of hypotheses about the phylogenetic relationships of the organisms in question and the subsequent inference of their geographic relationships; the second advocates a theory which does not have a precise deductive link with phylogenetic construction and often results in wildly narratative-type hypotheses. The vicariance approach de-emphasizes the concepts of centers of origin and dispersal and attempts to analyse distribution patterns in terms of subdivision (vicariance) of ancestral biotas. The development of the theory of plate tectonics and its universal acceptance enormously stimulate biogeographers to look at the world's continents and oceans from a mobilist point, which, along with the establishment of the rigorous tool of the phylogenetic analysis (cladistics), profoundly reshapes the above three theories. Hybridization and polyploidy are outstanding features of many plant groups. But hybridization, or reticulate evolution, is inconsistent with the basic concepts of cladistics which is an ever-branching pattern. Cladists have suggested several approaches. One of them analyses all the taxa by a standard cladistic procedure and closely examines the cladograms for polytomies and character conflicts that may indicate possible hybrids. Such generated hypothesis of hybridization can be corroborated or falsified by other forms of data, such as distribution, polyploidy, karyotype and pollen fertility. There are three criteria to justify a theory to be scientific: a) whether it is a theory composed of hypotheses strictly falsifiable; b) whether it has predictive effect; and c) whether it has a explanatory value. Cladistic systematics aims at generating cladograms, which are hypotheses of the nested pattern of synapomorphy, phylogenetic process and phyletic relationships, susceptible to testing by postulated synapomorphies. The predictive effect of systematics relies on the acceptance of hypotheses of congruence about the correlation of characters, which has been well founded. For non-systematic biologists, phylogenetic classification can be used as axiom to form a preliminary and fundamental explanation.     

The Use of Functional and Adaptive Criteria in Phylogenetic Systematics

SYNOPSIS. The controversy over whether functional data can contributeto phylogenetic inference has grown in recent years. Steps canbe taken toward its resolution if the relevance of functionaldata is judged for each component of phylogenetic analysis.These components are (1)recognizing of basic taxa (species orsupraspecific taxa), (2) formulating hypotheses of homologyfollowed by character analysis, (3) evaluating character phylogeny,(4) formulating phylogenetic hypotheses, and (5) evaluatingalternative phylogenetic hypotheses. It can be shown that functionaldata do not play a necessary or unique role in any of thesecomponents of phylogenetic analysis. Arguments to the contraryhave failed to provide a rigorous, repeatable methodto incorporatefunctional data; proponents of a functional approach to phylogeneticreconstruction rely too often on subjective, authoritarian argumentation. Students of functional evolutionary morphology frequently havefailed to understand the kinds of information necessary to studyor apply the causal process of adaptation via natural selection.This information, required by the very nature of the theoryitself, includes knowing the pattern of heredity of the phenotypiccharacters being studied, relating intrapopulational phenotypicvariability to variation in fitness, and knowing a sufficientamount about population structure to specify the componentsof natural selection. Studies within functional evolutionarymorphology are not designed to satisfy these requirements. Functionalevolutionary morphology uses the concepts of adaptation andnatural selection axiomatically, and thus such studies contributenothing to our understanding of the evolutionary process becausehypotheses about that process are not being evaluated. Thisalso suggests that, if functional evolutionary morphology wishesto engage in analyses of the evolutionary dynamics of the phenotype,a reorientation of its research strategy and goals will be necessary.     

On adaptation, the assessment of adaptations, and the value of adaptive arguments in phylogenetic reconstruction

Evolutionary adaptation concerns a relative concept and the study of adaptations is directed to structures of individuals. The concept is devoid of any meaning when it is applied to species or populations. Adaptation is not synonymous with fitness or survival but does contribute to both of them. The term adaptation has a dual meaning since it refers both to the process of adaptation and to the state of being adapted. In the process of adaptation the mechanism of natural selection takes a prominent position. But the operation and effectiveness of natural selection are constrained by various limiting factors. Besides that, features may also be the result of nonadaptive evolution and only attain their present adaptive function at a later point in time. Another possibility is that features have at present a function different from the one for which they were initially designed. With respect to the state of being, the study of adaptation attempts to examine whether a particular feature indeed forms an adequate response to selection forces from the environment. Five methods or approaches generally are used to assess the adaptive significance of features, viz. the comparative, correlation, optimization, cladistic, and synthetic approach. Only the last-mentioned approach forms an adequate method since it attempts to establish, by direct analysis, which well-defined selection force exerts its influence on a certain character. The practicing taxonomist is faced with the problem that the data necessary to apply the synthetic method, generally require detailed field studies. Not all evolutionary changes are under the influence of natural selection. The presence of some features may be based on entirely different mechanisms, such as genetic drift, mutational pressure, pleiotropic gene action, allometric growth, or ecophenotypic responses. Various problems inherent to the optimization approach, and several others of practical and theoretical nature, make the morphocline method of the functional and evolutionary morphologists unsuitable as a method for phylogenetic reconstruction.     

Foundations of the new phylogenetics

Evolutionary idea is the core of the modern biology. Due to this, phylogenetics dealing with historical reconstructions in biology takes a priority position among biological disciplines. The second half of the 20th century witnessed growth of a great interest to phylogenetic reconstructions at macrotaxonomic level which replaced microevolutionary studies dominating during the 30s-60s. This meant shift from population thinking to phylogenetic one but it was not revival of the classical phylogenetics; rather, a new approach emerged that was baptized The New Phylogenetics. It arose as a result of merging of three disciplines which were developing independently during 60s-70s, namely cladistics, numerical phyletics, and molecular phylogenetics (now basically genophyletics). Thus, the new phylogenetics could be defined as a branch of evolutionary biology aimed at elaboration of "parsimonious" cladistic hypotheses by means of numerical methods on the basis of mostly molecular data. Classical phylogenetics, as a historical predecessor of the new one, emerged on the basis of the naturphilosophical worldview which included a superorganismal idea of biota. Accordingly to that view, historical development (the phylogeny) was thought an analogy of individual one (the ontogeny) so its most basical features were progressive parallel developments of "parts" (taxa), supplemented with Darwinian concept of monophyly. Two predominating traditions were diverged within classical phylogenetics according to a particular interpretation of relation between these concepts. One of them (Cope, Severtzow) belittled monophyly and paid most attention to progressive parallel developments of morphological traits. Such an attitude turned this kind of phylogenetics to be rather the semogenetics dealing primarily with evolution of structures and not of taxa. Another tradition (Haeckel) considered both monophyletic and parallel origins of taxa jointly: in the middle of 20th century it was split into phylistics (Rasnitsyn's term; close to Simpsonian evolutionary taxonomy) belonging rather to the classical realm, and Hennigian cladistics that pays attention to origin of monophyletic taxa exclusively. In early of the 20th century, microevolutionary doctrine became predominating in evolutionary studies. Its core is the population thinking accompanied by the phenetic one based on equation of kinship to overall similarity. They were connected to positivist philosophy and hence were characterized by reductionism at both ontological and epistemological levels. It led to fall of classical phylogenetics but created the prerequisites for the new phylogenetics which also appeared to be full of reductionism. The new rise of phylogenetic (rather than tree) thinking during the last third of the 20th century was caused by lost of explanatory power of population one and by development of the new worldview and new epistemological premises. That new worldview is based on the synergetic (Prigoginian) model of development of non-equilibrium systems: evolution of the biota, a part of which is phylogeny, is considered as such a development. At epistemological level, the principal premise appeared to be fall of positivism which was replaced by post-positivism argumentation schemes. Input of cladistics into new phylogenetics is twofold. On the one hand, it reduced phylogeny to cladistic history lacking any adaptivist interpretation and presuming minimal evolution model. From this it followed reduction of kinship relation to sister-group relation lacking any reference to real time scale and to ancestor-descendant relation. On the other hand, cladistics elaborated methodology of phylogenetic reconstructions based on the synapomorphy principle, the outgroup concept became its part. The both inputs served as premises of incorporation of both numerical techniques and molecular data into phylogenetic reconstruction. Numerical phyletics provided the new phylogenetics with easily manipulated algorithms of cladogram construing and thus made phylogenetic reconstructions operational and repetitive. The above phenetic formula "kinship = similarity" appeared to be a keystone for development of the genophyletics. Within numerical phyletics, a lot of computer programs were elaborated which allow to manipulate with evolutionary scenario during phylogenetic reconstructions. They make it possible to reconstruct both clado- and semogeneses based on the same formalized methods. Multiplicity of numerical approaches indicates that, just as in the case of numerical phenetics, choice of adequate method(s) should be based on biologically sound theory. The main input of genophyletics (= molecular phylogenetics) into the new phylogenetics was due to completely new factology which makes it possible to compare directly such far distant taxa as prokaryotes and higher eukaryotes. Genophyletics is based on the theory of neutral evolution borrowed from microevolutionary theory and on the molecular clock hypothesis which is now considered largely inadequate. The future developments of genophyletics will be aimed at clarification of such fundamental (and "classical" by origin) problems as application of character and homology concepts to molecular structures. The new phylogenetics itself is differentiated into several schools caused basically by diversity of various approaches existing within each of its "roots". Cladistics makes new phylogenetics splitted into evolutionary and parsimonious ontological viewpoints. Numerical phyletics divides it into statistical and (again) parsimonious methodologies. Molecular phylogenetics is opposite by its factological basis to morphological one. The new phylogenetics has significance impact onto the "newest" systematics. From one side, it gives ontological status back to macrotaxa they have lost due to "new" systematics based on population thinking. From another side, it rejects some basical principles of classical phylogenetic (originally Linnean) taxonomy such as recognitions of fixed taxonomic ranks designated by respective terms and definition of taxic names not by the diagnostic characters but by reference to the ancestor. The latter makes the PhyloCode overburdened ideologically and the "newest" systematics self-controversial, as concept of ancestor has been acknowledged non-operational from the very beginning of cladistics. Relation between classical and new phylogenetics is twofold. At the one hand, general phylogenetic hypothesis (in its classical sense) can be treated as a combination of cladogenetic and semogenetic reconstructions. Such a consideration is bound to pay close attention to the uncertainty relation principle which, in case of the phylogenetics, means that the general phylogenetic hypothesis cannot be more certain than any of initial cladogenetic or semogenetic hypotheses. From this standpoint, the new phylogenetics makes it possible to reconstruct phylogeny following epistemological principle "from simple to complex". It elaborates a kind of null hypotheses about evolutionary history which are more easy to test as compared to classical hypotheses. Afterward, such hypotheses are possible to be completed toward the classical, more content-wise ones by adding anagenetic information to the cladogenetic one. At another hand, reconstructions elaborated within the new phylogenetics could be considered as specific null hypotheses about both clado- and semogeneses. They are to be tested subsequently by mean of various models, including those borrowed from "classical" morphology. The future development of the new phylogenetics is supposed to be connected with getting out of plethora of reductionism inherited by it from population thinking and specification of object domain of the phylogenetics. As the latter is a part of an evolutionary theory, its future developments will be adjusted with the latter. Lately predominating neodarwinism is now being replaced by the epigenetic evolutionary theory to which phylistics (one of the modern versions of classical phylogenetics) seems to be more correspondent.     

Parsimony in evolutionary theory: Law or methodological prescription?

Parsimony (Ockham's razor) is in widespread use in phylogenetic reconstruction (evolution takes the shortest route), however it is not quite obvious which is the rank that this principle should have in evolutionary theory. Parsimony is not of a single kind but, on the contrary, is at least of two kinds: ontological and methodological. Ontological parsimony involves an assumption about the “simplicity of nature”. Methodological parsimony is a purely logical precept, a case of the broad practical principle not to believe anything for which there is no evidence. The two kinds of parsimony are not compatible with one another. The ontological hypotheses that reality is simple has been refuted many times in the history of science, and evolution is not an exception to this. In spite of the fact, that direct evolutionary changes have higher probability than the ones that take “unnecessary” steps, evolutionary parsimony is merely a methodological precept, not a law of evolution. Probability is not enough to give evolutionary parsimony a rank of ontological axiom. Therefore, the reasons to use the principle of evolutionary parsimony are only methodological. A definition of evolutionary parsimony is: as long as no evidence is available to suggest an alternative pathway evolution may be considered to occur in the most parsimonious way.     

Optimierung und ökonomisierung im kontext von evolutionstheorie und phylogenetischer rekonstruktion

The meaning of optimality and economy in phylogenetics and evolutionary biology is discussed. It can be shown that the prevailing concepts of optimality and economy are equivocal as they are not based on strict theoretical positions and as they have a variable meaning in different theoretical contexts. The ideas of optimality and economy can be considered to be identical with the expectation of a relatively simple order in a particular field of study. Although there exists no way of inferring one or several methods of solving scientific problems from the presupposed idea of economy and optimality, a lack of motivation for scientific investigations would result if the concepts of economy and optimality in nature were dropped. By reference to several examples, it is shown that the concepts of optimality and economy are only useful against the background of indispensable theories. If there is a shift from one theory to another, a restriction on the use of these concepts is necessary. Optimality and economy in the sense of operations research in engineering or economical sciences depend on the principle of minimum costs. Both theoretical concepts: technical efficiency in relation to the energy required to run a machine and profit maximation in an economical framework must be shown to be realistic assumptions. In the field of biology processes of optimization and economization are normally discussed under two different views:

1. The concept of economy is used in cases of functional adaptation when the organism makes good use of the building material which is available to fulfill one (or more) functions. The theoretical background must be seen in the energy-consuming aspect of the organism.
2. In evolutionary change and phylogeny ‘economization’ and ‘optimization’ are deduced from the evolutionary theory, and evolution is shown to produce a special kind of biological economy in biological systems (Bock & von Wahlert, 1965). The ‘Okonomie-Prinzip’ or ‘Lesrichtungskriterium’ points out the arguments needed to state a phylogenetic theory and to construct a dendrogram (Peters & Gutmann, 1971).

In every phylogenetic theory concerning the adaptational change in the evolving biological system an explanation for the function of all stages is required. Only those statements should be accepted as phylogenetic theories which are characterized by the demonstration of the process of economization in the functional relations of the evolving organism. The process of adaptation can be determined by the improved chance of some mutants to propagate their genetical information. In this process all functional systems in their interrelations — i.a. mutual dependence — and their relation with the environment add their functional efficiency to the information to be delivered to their progeny, because the more economical biological system in a certain environment will have a better chance to produce offspring. This outcome is affirmed by natural selection which works on all levels of the evolving biological systems (Gutmann & Peters 1973). Nevertheless a judgment about adaptation cannot be taken as a scale of measurement in the phylogenetic process. The conditions in the organism itself and in the environment or in the organic system alone can change in so profound a manner that the marginal conditions of the earlier stages of the process of adaptation are not the same as in the derived ones. During phylogenetic change of the evolving organism the selective strains are also continuously changing. As a consequence no state or invariant concept of economy can cover the different stages of the phylogenetic process. The pragmatical meaning of the theoretical consideration is substantiated by the example of the hydrostatic skeleton theory in which the chordates are derived from metameric worms with a fluid skeleton. Herrn Professor Dr. P. Dullemeijer sind die Verfasser für kritische Lektüre und wertovolle Hinweise zu Dank verpflichtet.     

FROM MORE TO FEWER? TESTING AN ALLEGEDLY PERVASIVE TREND IN THE EVOLUTION OF MORPHOLOGICAL STRUCTURE

While evolutionary trends have long received much attention and have been widely disputed, new methods are now allowing the testing of directional hypotheses with increased rigor. Here, we test a general hypothesis about the way many kinds of discrete characters are thought to evolve, termed oligomerization. This is the tendency for serial structures (such as arthropod body and appendage segments) or armature (such as spines) to evolve primarily through loss and fusion. Focusing on the Crustacea, we use maximum likelihood methods to test for directional evolution in a large sample (> 500) of discrete traits, analyzed against molecular-based phylogenies. We find evidence for a significant trend toward trait loss, in accordance with the reduction principle. However, this trend is far from ubiquitous, with many characters exhibiting a reconstructed bias toward gains. These results suggest that caution must be used before drawing conclusions about which taxa are "primitive" or about the directionality of morphological shifts in the absence of phylogenetic analysis. Nevertheless, oligomerization-as a trend rather than a law-may be an important process that influences evolutionary trajectories from both morphological and functional perspectives.     

Adaptations and history

The historical definition of adaptations has come into wide use as comparative biologists have applied methods of phylogenetic analysis to a variety of evolutionary problems. Here we point out a number of difficulties in applying historical methods to the study of adaptation, especially in cases where a trait has arisen but once. In particular, the potential complexity of the genetic correlations among phenotypic traits, performance variables and fitness makes inferring past patterns of selection from comparative data difficult. A given pattern of character distribution may support many alternative hypotheses of mechanism. While phylogenetic data are limited in their ability to reveal evolutionary mechanisms, they have always been an important source of adaptive hypotheses and will continue to be so.     

TESTING FOR UNEQUAL AMOUNTS OF EVOLUTION IN A CONTINUOUS CHARACTER ON DIFFERENT BRANCHES OF A PHYLOGENETIC TREE USING LINEAR AND SQUARED-CHANGE PARSIMONY: AN EXAMPLE USING LESSER ANTILLEAN ANOLIS LIZARDS

Although a large body of work investigating tests of correlated evolution of two continuous characters exists, hypotheses such as character displacement are really tests of whether substantial evolutionary change has occurred on a particular branch or branches of the phylogenetic tree. In this study, we present a methodology for testing such a hypothesis using ancestral character state reconstruction and simulation. Furthermore, we suggest how to investigate the robustness of the hypothesis test by varying the reconstruction methods or simulation parameters. As a case study, we tested a hypothesis of character displacement in body size of Caribbean Anolis lizards. We compared squared-change, weighted squared-change, and linear parsimony reconstruction methods, gradual Brownian motion and speciational models of evolution, and several resolution methods for linear parsimony. We used ancestor reconstruction methods to infer the amount of body size evolution, and tested whether evolutionary change in body size was greater on branches of the phylogenetic tree in which a transition from occupying a single-species island to a two-species island occurred. Simulations were used to generate null distributions of reconstructed body size change. The hypothesis of character displacement was tested using Wilcoxon Rank-Sums. When tested against simulated null distributions, all of the reconstruction methods resulted in more significant P-values than when standard statistical tables were used. These results confirm that P-values for tests using ancestor reconstruction methods should be assessed via simulation rather than from standard statistical tables. Linear parsimony can produce an infinite number of most parsimonious reconstructions in continuous characters. We present an example of assessing the robustness of our statistical test by exploring the sample space of possible resolutions. We compare ACCTRAN and DELTRAN resolutions of ambiguous character reconstructions in linear parsimony to the most and least conservative resolutions for our particular hypothesis.     

Testing evolutionary hypotheses about human biological adaptation using cross-cultural comparison

Physiological data from a range of human populations living in different environments can provide valuable information for testing evolutionary hypotheses about human adaptation. By taking into account the effects of population history, phylogenetic comparative methods can help us determine whether variation results from selection due to particular environmental variables. These selective forces could even be due to cultural traits-which means that gene-culture co-evolution may be occurring. In this paper, we outline two examples of the use of these approaches to test adaptive hypotheses that explain global variation in two physiological traits: the first is lactose digestion capacity in adults, and the second is population sex-ratio at birth. We show that lower than average sex ratio at birth is associated with high fertility, and argue that global variation in sex ratio at birth has evolved as a response to the high physiological costs of producing boys in high fertility populations.     

Cross-Testing Adaptive Hypotheses: Phylogenetic Analysis and the Origin of Bird Flight

Adaptive scenarios in evolutionary biology have always beenbased on incremental improvements through a series of adaptivestages. But they have often been justified by appeal to assumptionsof how natural selection must work or by appeal to optimalityarguments or notions of evolutionary process. Cladistic methodology,though it cannot logically falsify hypotheses of process, provideshypotheses of evolutionary pattern independent of other considerationsand so provides a useful test of consilience with genealogy.I illustrate the cross-test of hypotheses of the evolution ofseveral functions and adaptations related to the origin of birdflight with independently derived phylogenetic analysis. Consiliencedoes not support ideas that the close ancestors of birds werearboreal or evolved flight from the trees, nor that they werephysiologically intermediate between typical reptiles and livingbirds, nor that feathers evolved for flight. Rather, the ancestorsof birds were terrestrial, they were fast-growing, active animals,and the original functions of feathers were in insulation andcoloration.     

THE EFFECT OF ORDERED CHARACTERS ON PHYLOGENETIC RECONSTRUCTION

Abstract Morphological structures are likely to undergo more than a single change during the course of evolution. As a result, multistate characters are common in systematic studies and must be dealt with. Particularly interesting is the question of whether or not multistate characters should be treated as ordered (additive) or unordered (non-additive). In accepting a particular hypothesis of order, numerous others are necessarily rejected. We review some of the criteria often used to order character states and the underlying assumptions inherent in these criteria.
The effects that ordered multistate characters can have on phylogenetic reconstruction are examined using 27 data sets. It has been suggested that hypotheses of character state order are more informative then hypotheses of unorder and may restrict the number of equally parsimonious trees as well as increase tree resolution. Our results indicate that ordered characters can produce more, equal or less equally parsimonious trees and can increase, decrease or have no effect on tree resolution. The effect on tree resolution can be a simple gain in resolution or a dramatic change in sister-taxa relationships. In cases where several outgroups are included in the data matrix, hypotheses of order can change character polarities by altering outgroup topology. Ordered characters result in a different topology from unordered characters only when the hierarchy of the cladogram disagrees with the investigator's a priori hypothesis of order. If the best criterion for assessing character evolution is congruence with other characters, the practice of ordering multistate characters is inappropriate.     

LineageSpecificSeqgen: generating sequence data with lineage-specific variation in the proportion of variable sites

Background  

Commonly used phylogenetic models assume a homogeneous evolutionary process throughout the tree. It is known that these homogeneous models are often too simplistic, and that with time some properties of the evolutionary process can change (due to selection or drift). In particular, as constraints on sequences evolve, the proportion of variable sites can vary between lineages. This affects the ability of phylogenetic methods to correctly estimate phylogenetic trees, especially for long timescales. To date there is no phylogenetic model that allows for change in the proportion of variable sites, and the degree to which this affects phylogenetic reconstruction is unknown.     

Mapping cladograms into morphospaces

In cladistic analyses, taxa are grouped hierarchically into clades according to shared apomorphic character states to construct cladograms; cladograms are interpretable as phylogenetic hypotheses. In morphological space analyses, organism forms are represented as points in morphospaces; point proximities in morphospaces represent similarities that might be attributable to phenetic convergence and, consequently, may correspond inaccurately with hypothesized evolutionary relationships. A method for synthesizing phylogenetic results that are interpreted from cladistic analyses with phenetic results that are obtained from morphological space analyses is presented here; in particular, points that represent forms typifying taxa in morphospace are assigned as terminal nodes for appropriate cladograms that are mapped into morphospaces by positioning nonterminal nodes and orienting internodes according to a geometric algorithm. Nonterminal nodes may be interpreted as ancestors in phylogenetic hypotheses and occupy positions that represent particular organism forms in morphospaces. By mapping cladograms into morphospaces, therefore, evolutionary morphologists can reconstruct ancestral morphologies and test historical transformation hypotheses.     

Assessing current adaptation and phylogenetic inertia as explanations of trait evolution: the need for controlled comparisons

The determination of whether the pattern of trait evolution observed in a comparative analysis of species data is due to adaptation to current environments, to phylogenetic inertia, or to both of these forces requires that one control for the effects of either force when making an assessment of the evolutionary role of the other. Orzack and Sober (2001) developed the method of controlled comparisons to make such assessments; their implementation of the method focussed on a discretely varying trait. Here, we show that the method of controlled comparisons can be viewed as a meta-method, which can be implemented in many ways. We discuss which recent methods for the comparative analysis of continuously distributed traits can generate controlled comparisons and can thereby be used to properly assess whether current adaptation and/or phylogenetic inertia have influenced a trait's evolution. The implementation of controlled comparisons is illustrated by an analysis of sex-ratio data for fig wasps. This analysis suggests that current adaptation and phylogenetic inertia influence this trait.     

Conceptual issues in local adaptation

Studies of local adaptation provide important insights into the power of natural selection relative to gene flow and other evolutionary forces. They are a paradigm for testing evolutionary hypotheses about traits favoured by particular environmental factors. This paper is an attempt to summarize the conceptual framework for local adaptation studies. We first review theoretical work relevant for local adaptation. Then we discuss reciprocal transplant and common garden experiments designed to detect local adaptation in the pattern of deme × habitat interaction for fitness. Finally, we review research questions and approaches to studying the processes of local adaptation – divergent natural selection, dispersal and gene flow, and other processes affecting adaptive differentiation of local demes. We advocate multifaceted approaches to the study of local adaptation, and stress the need for experiments explicitly addressing hypotheses about the role of particular ecological and genetic factors that promote or hinder local adaptation. Experimental evolution of replicated populations in controlled spatially heterogeneous environments allow direct tests of such hypotheses, and thus would be a valuable way to complement research on natural populations.