Systematics as science: A response to Cronquist

Our reply to the commentary on cladistics presented by Cronquist (1987) is aimed at four issues:

1. the application of scientific principles in systematics;
2. the recognition that the analysis of pattern is a vital precursor to any consideration of evolutionary process. A priori judgements of evolutionary process are unnecessary for the generation of informative systematic hypotheses which are chosen for their ability to explain the patterns of character distributions rather than for compatibility with any particular preconceived ideas about evolution;
3. that phenetic concepts such as overall similarity, grades, gaps, and degree of divergence, if included in methods of phylogenetic inference, will give erroneous results. Paraphyletic and polyphyletic groups must, consequently, be rejected from systematics since they have no rational empirical basis for recognition;
4. the fact that many of the problems of phylogenetic analysis attributed by Cronquist to cladistics are common to all systematic methods but that these can be dealt with by the application of such principles as parsimony, synapomorphy, and strict monophyly.

     

Gene trees and species trees – mutual influences and interdependences of population genetics and systematics

Both population genetics and systematics are core disciplines of evolutionary biology. While systematics deals with genealogical relationships among taxa, population genetics has mainly been based on allele frequencies and the distribution of genetic variants whose genealogical relations could for a long time, due mainly to methodological constraints, not be inferred. The advent of mitochondrial DNA analyses and modern sequencing techniques in the 1970s revolutionized evolutionary genetic studies and gave rise to molecular phylogenetics. In the wake of this new development systematic approaches and principles were incorporated into intraspecific studies at the population level, e.g. the concept of monophyly which is used to delineate evolutionarily significant units in conservation biology. A new discipline combining phylogenetic analyses of genetic lineages with their geographic distribution ('phylogeography') was introduced as an explicit synthesis of population genetics and systematics. On the other hand, it has increasingly become obvious that discordances between gene trees and species trees not only result from spurious data sets or methodological flaws in phylogenetic analyses, but that they often reflect real population genetic processes such as lineage sorting or hybridization. These processes have to be taken into account when evaluating the reliability of gene trees to avoid wrong phylogenetic conclusions. The present review focuses on the phenomenon of non-phylogenetic sorting of ancestral polymorphisms, its probability and its consequences for molecular systematics.     

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.     

Parallelism,parsimony, and the phytogeny of the lemuridae

In spite of the increasing popularity of cladistic methods in studies of primate systematics, few authors have investigated the effects of parallel evolution when such methods are applied to empirical data. To counter the effects of parallelism, cladistic techniques rely on the principle of evolutionary parsimony. When parsimony procedures are used to reconstruct the phylogeny of the Lemuridae, nine highly parsimonious phylogenies can be deduced. Further choice among these competing hypotheses of relationship is determined by the extent to which one embraces the parsimony principle. The phylogeny obtained by the most rigorous adherence to the parsimony principle is one which is wholly consistent with traditional evolutionary classifications of the Lemuridae. Moderate levels of parallelism can lead to the generation of several plausible, alternative phylogenetic hypotheses; less than 25% of the characters analyzed here need have evolved in parallel, yet they are largely responsible for the ambiguity of the nine different lemurid phylogenies. This suggests that phylogeny reconstructions based entirely on cladistic methods do not provide a suitable basis for the construction of classifications for groups such as the order Primates, where the degree of parallelism is likely to be quite high.     

Integrative taxonomy,or iterative taxonomy?

The recently introduced term ‘integrative taxonomy’ refers to taxonomy that integrates all available data sources to frame species limits. We survey current taxonomic methods available to delimit species that integrate a variety of data, including molecular and morphological characters. A literature review of empirical studies using the term ‘integrative taxonomy’ assessed the kinds of data being used to frame species limits, and methods of integration. Almost all studies are qualitative and comparative – we are a long way from a repeatable, quantitative method of truly ‘integrative taxonomy’. The usual methods for integrating data in phylogenetic and population genetic paradigms are not appropriate for integrative taxonomy, either because of the diverse range of data used or because of the special challenges that arise when working at the species/population boundary. We identify two challenges that, if met, will facilitate the development of a more complete toolkit and a more robust research programme in integrative taxonomy using species tree approaches. We propose the term ‘iterative taxonomy’ for current practice that treats species boundaries as hypotheses to be tested with new evidence. A search for biological or evolutionary explanations for discordant evidence can be used to distinguish between competing species boundary hypotheses. We identify two recent empirical examples that use the process of iterative taxonomy.     

Life history evolution of marine invertebrates: New views from phylogenetic systematics

Established theories on the evolution of the diverse life histories of marine metazoans, specifically invertebrates, were developed in the absence of rigorous phylogenetic methods. With improved estimates of evolutionary relationships for various marine invertebrate groups, based on phylogenetic systematics, we can now critically evaluate the assumptions upon which these theories are based. Several studies emphasizing a phylogenetic systematics approach have recently examined the evolutionary transitions among reproductive traits and challenge us to reconsider the generality of the assumptions made about life history evolution. The results point towards exciting possibilities for a better understanding of the great diversity of reproductive and developmental modes we observe in marine invertebrates today.     

The evolution of avian migration

The study of avian migration has reached sophisticated levels in many areas, including ecology, behaviour, and physiology. Traditional discussions of the evolution of migration, however, have been compromised for several reasons. Previous ideas concerning the ancestral home of migrant species, southern or northern, and whether a partially migratory stage always precedes a fully migratory stage, were not expressed as testable hypotheses. Plotting migratory behaviour on phylogenetic trees has become commonplace and allows tests of traditional hypotheses. Some of these studies are reviewed, lending some support for almost all of the previous ideas. Although phylogenetic mapping helps to frame questions about the evolution of migration in a testable framework, there are two serious issues. First, experimental and observational studies reveal that the expression of migratory behaviour can change rapidly within a lineage, which can violate assumptions of character mapping. In addition, a species distribution model is used to show that current conditions for obligate migratory populations of the chipping sparrow were much restricted at the Last Glacial Maximum, and that the species might have been considered a partial migrant at that time. The expression of migratory behaviour in an extant species might be an artefact of the current inter‐glacial period. Only if the rate of gains and losses of migratory behaviour can be incorporated into a phylogenetic mapping exercise will the actual evolutionary pattern of migration be revealed. For example, reconstruction of the ancestral area and the evolutionary history of migratory categories in a clade of New World warblers depended on the assumptions of character state transitions. A second concern is that the trait ‘migratory’ is too broad for evolutionary analysis and that, if possible, the expression of hyperphagia, Zugunruhe, and navigation could be mapped individually. Loss or suppression of any of these components can lead to sedentary populations, revealing how migratory behaviour can appear and disappear rapidly. A report of low levels of Zugunruhe in a sedentary bird, Saxicola torquata, is reconstructed as derived in a clade of otherwise migratory populations, suggesting that the loss of migration was a result of suppression (but not elimination) of Zugunruhe. When researchers mention the independent origin of migration in a clade, they are most likely referring to the gain or loss of the expression of the ancestral migratory programme, not the de novo evolution of migration per se. © 2011 The Linnean Society of London, Biological Journal of the Linnean Society, 2011, 104 , 237–250.     

The phylogenetic position of the Clitellata and the Echiura - on the problematic assessment of absent characters*

Absent characters (negative characters) are difficult to assess and their correct interpretation as symplesiomorphies, synapomorphies or convergencies (homoplasies) is one of the greatest challenges in phylogenetic systematics. Different phylogenetic assessments often result in contradictory phylogenetic hypotheses, in which the direction of evolutionary changes is diametrically opposed. Especially in deciding between primary (plesiomorphic) and secondary (apomorphic) absence, false conclusions may be reached if only the outgroup comparison and the principle of parsimony are employed without attempting any biological evaluation or interpretation of characters. For example, in the higher‐level systematization of the Annelida and related taxa different assessments of absent characters have led to conflicting hypotheses about the phylogenetic relationships and the ground pattern of the annelid stem species. Varying phylogenetic interpretations regarding the absence of the chemosensory nuchal organs in the clitellates and their presence in polychaetes initiated a controversy that produced two alternative phylogenetic hypotheses: (1) the Clitellata are highly derived Annelida related to a subtaxon within the, in this case, paraphyletic ‘Polychaeta’ or (2) the Clitellata are comparatively primitive Annelida representing the sister group of a monophyletic taxon Polychaeta. In the former, the absence of nuchal organs in the Clitellata is regarded as a secondary character, in the latter as primary. As most Clitellata are either limnetic or terrestrial, we must ask which characters are plesiomorphies, taken from their marine stem species without changes. In addition to a thorough investigation and evaluation of clitellate characters, a promising approach to these questions is to look for such characters in limnetic and terrestrial annelids clearly not belonging to the Clitellata. A similar problem applies to the evaluation of the position of the Echiura, which lack both segmentation and nuchal organs. Evidence is presented that in both taxa these absent characters represent derived, apomorphic character states. The consequences for their phylogenetic position and the questionable monophyly of the Polychaeta are discussed. The conclusion drawn from morphological character assessments is in accordance with recently published hypotheses based on molecular data.     

Studies in cave life evolution: a rationale for future theoretical developments using phylogenetic inference

As in every field of comparative biology, phylogeny provides an independent reference system in studies on cave life evolution to test current theoretical proposals. Using phylogeny, sound hypotheses on the ancestral states of characters and their subsequent changes can be made by polarizing the characters between related taxa. Hypotheses on evolutionary processes can also be tested by comparing the patterns they imply with independently inferred phylogenetic patterns. The power of the tests relies upon the independence of phylogenetic patterns (built with cladistics using Wagner parsimony) and the theoretical proposals under study. Classical assumptions on the evolution of troglobitic life are analysed with this methodology. The following points are discussed: what is a troglobitic taxon? Are there features characteristic of troglobitic taxa? Is troglobitic life an evolutionary dead end? What circumstances favour troglobitic evolution? Using phylogenetic analysis, the presence or absence of so-called troglomorphic features were inferred in troglobitic taxa. In fact these taxa can be characterized only by their behavioural ecology. Pre-adaptations (exaptations) can also be precisely defined. Cave living does not appear to be an evolutionary dead end. Two patterns subsequent to cave life appearance have been documented: speciation of troglobitic taxa in the subterranean environment, and reversal to an epigean habitat. Troglobitic life thus turns out to be one step in the diversification of clades. Troglobitic life is usually explained as an evolution under the pressure of unfavourable environmental conditions, or the conquest of a new resource, or the result of biological interactions (competition, predation). Phylogenetic analyses show that none of these hypotheses propose clear alternatives on cave life evolution. Moreover most of their a priori statements cannot easily be falsified. As such they have only limited explanatory power.     

Phylogenetics in the bioinformatics culture of understanding

Bioinformatics, as a relatively young discipline, has grown up in a world of high-throughput large volume data that requires automatic analysis to enable us to stay on top of it all. As a response, the bioinformatics discipline has developed strategies to find patterns in a 'low signal : noise ratio' environment. While the need to process large amounts of information and extract hypotheses is both laudable and inescapable, the pressures that such requirements have introduced can lead to short cuts and misapprehensions. This is particularly the case with reference to assumptions about the underlying evolutionary theories that are implicitly invoked by the algorithms utilised in the analysis pipelines. The classic example is the misuse of the term 'homologous' to mean 'similar' or even 'functionally similar', rather than the correct definition of 'having the same evolutionary origin', which may or may not imply similarity of function. In this review, we outline some of the common phylogenetic questions from a bioinformatics perspective that can be better addressed with a deeper understanding of evolutionary principles and show, with examples from the amidohydrolase and Toll families, that quite different conclusions can be drawn if such approaches are taken. This review focuses on the importance of the underlying evolutionary biology, rather than assessing the merits of different phylogenetic techniques. The relative merits of a priori and a posteriori inclusion of biological information are discussed.     

The role of parsimony,outgroup analysis,and theory of evolution in phylogenetic systematics

It is argued that both the principle of parsimony and the theory of evolution, especially that of natural selection, are essential analytical tools in phylogenetic systematics, whereas the widely used outgroup analysis is completely useless and may even be misleading. In any systematic analysis, two types of patterns of characters and character states must be discriminated which are referred to as completely and incompletely resolved. In the former, all known species are presented in which the characters and their states studied occur, whereas in the latter this is not the case. Dependent on its structure, a pattern of characters and their states may be explained by either a unique or by various conflicting, equally most parsimonious hypotheses of relationships. The so-called permutation method is introduced which facilitates finding the conflicting, equally most parsimonious hypotheses of relationships. The utility of the principle of parsimony is limited by the uncertainty as to whether its application in systematics must refer to the minimum number of steps needed to explain a pattern of characterts and their states most parsimoniously or to the minimum number of evolutionary events assumed to have caused these steps. Although these numbers may differ, the former is usually preferred for simplicity. The types of outgroup analysis are shown to exist which are termed parsimony analysis based on test samples and cladistic type of outgroup analysis. Essentially, the former is used for analysing incompletely resolved patterns of characters and their states, the latter for analysing completely resolved ones. Both types are shown to be completely useless for rejecting even one of various conflicting, equally most parsimonious hypotheses of relationships. According to contemporary knowledge, this task can be accomplished only by employing the theory of evolution (including the theory of natural selection). But even then, many phylogenetic-systematic problems will remain unsolved. In such cases, arbitrary algorithms like those offered by phenetics can at best offer pseudosolutions to open problems. Despite its limitations, phylogenetic systematics is superior to any kind of aphylogenetic systematics (transformed cladistics included) in approaching a (not: the) “general reference system” of organisms.     

Phylogenetics and the future of helminth systematics

Phylogenetic systematics is a relatively new formal technique that increases the precision with which one can make direct estimates of the history of phylogenetic descent. These estimates are made in the form of phylogenetic trees, or cladograms. Cladograms may be converted directly into classifications or they may be used to test various hypotheses about the evolutionary process. More than 20 phylogenetic analyses of helminth groups have been published already, and these have been used to investigate evolutionary questions in developmental biology, biogeography, speciation, coevolution, and evolutionary ecology.     

Towards resolving the complete fern tree of life

In the past two decades, molecular systematic studies have revolutionized our understanding of the evolutionary history of ferns. The availability of large molecular data sets together with efficient computer algorithms, now enables us to reconstruct evolutionary histories with previously unseen completeness. Here, the most comprehensive fern phylogeny to date, representing over one-fifth of the extant global fern diversity, is inferred based on four plastid genes. Parsimony and maximum-likelihood analyses provided a mostly congruent results and in general supported the prevailing view on the higher-level fern systematics. At a deep phylogenetic level, the position of horsetails depended on the optimality criteria chosen, with horsetails positioned as the sister group either of Marattiopsida-Polypodiopsida clade or of the Polypodiopsida. The analyses demonstrate the power of using a 'supermatrix' approach to resolve large-scale phylogenies and reveal questionable taxonomies. These results provide a valuable background for future research on fern systematics, ecology, biogeography and other evolutionary studies.     

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 Evolutionary Interplay of Social Behavior,Resource Use and Anti-Predator Behavior in Zetoborinae+ Blaberinae+Gyninae+Diplopterinae Cockroaches: A Phylogenetic Analysis

Theories of social evolution in cockroaches have mainly referred to hypotheses of evolutionary relationship between resource use and social system. The use of particular resources, such as scattered and enclosed habitat, was hypothesized to have favored evolution toward presociality or subsociality. A phylogenetic test of these hypotheses is carried out using the clade (Zetoborinae+ Blaberinae+Gyninae+Diplopterinae). Phylogenetic patterns of habitat use, social systems and anti-predator behavior are inferred and compared to previous evolutionary hypotheses. There is much heterobathmy concerning these three attributes and five evolutionary paths are inferred which weakly corroborate the hypothesis of evolutionary relationship between resource use and social system. Anti-predator behavior also appears to be possibly related evolutionarily to social systems.     

Palaeomorphology: fossils and the inference of cladistic relationships

Edgecombe, G.D. 2010. Palaeomorphology: fossils and the inference of cladistic relationships. —Acta Zoologica (Stockholm) 91 : 72–80 Twenty years have passed since it was empirically demonstrated that inclusion of extinct taxa could overturn a phylogenetic hypothesis formulated upon extant taxa alone, challenging Colin Patterson’s bold conjecture that this phenomenon ‘may be non‐existent’. Suppositions and misconceptions about missing data, often couched in terms of ‘wildcard taxa’ and ‘the missing data problem’, continue to cloud the literature on the topic of fossils and phylogenetics. Comparisons of real data sets show that no a priori (or indeed a posteriori) decisions can be made about amounts of missing data and most properties of cladograms, and both simulated and real data sets demonstrate that even highly incomplete taxa can impact on relationships. The exclusion of fossils from phylogenetic analyses is neither theoretically nor empirically defensible.     

The mechanistic,genetic and evolutionary causes of bird eye colour variation

Birds display a rainbow of eye colours, but this trait has been little studied compared with plumage coloration. Avian eye colour variation occurs at all phylogenetic scales: it can be conserved throughout whole families or vary within one species, yet the evolutionary importance of this eye colour variation is under-studied. Here, we summarize knowledge of the causes of eye colour variation at three primary levels: mechanistic, genetic and evolutionary. Mechanistically, we show that avian iris pigments include melanin and carotenoids, which also play major roles in plumage colour, as well as purines and pteridines, which are often found as pigments in non-avian taxa. Genetically, we survey classical breeding studies and recent genomic work on domestic birds that have identified potential ‘eye colour genes’, including one associated with pteridine pigmentation in pigeons. Finally, from an evolutionary standpoint, we present and discuss several hypotheses explaining the adaptive significance of eye colour variation. Many of these hypotheses suggest that bird eye colour plays an important role in intraspecific signalling, particularly as an indicator of age or mate quality, although the importance of eye colour may differ between species and few evolutionary hypotheses have been directly tested. We suggest that future studies of avian eye colour should consider all three levels, including broad-scale iris pigment analyses across bird species, genome sequencing studies to identify loci associated with eye colour variation, and behavioural experiments and comparative phylogenetic analyses to test adaptive hypotheses. By examining these proximate and ultimate causes of eye colour variation in birds, we hope that our review will encourage future research to understand the ecological and evolutionary significance of this striking avian trait.     

Bayesian molecular dating: opening up the black box

Molecular dating analyses allow evolutionary timescales to be estimated from genetic data, offering an unprecedented capacity for investigating the evolutionary past of all species. These methods require us to make assumptions about the relationship between genetic change and evolutionary time, often referred to as a ‘molecular clock’. Although initially regarded with scepticism, molecular dating has now been adopted in many areas of biology. This broad uptake has been due partly to the development of Bayesian methods that allow complex aspects of molecular evolution, such as variation in rates of change across lineages, to be taken into account. But in order to do this, Bayesian dating methods rely on a range of assumptions about the evolutionary process, which vary in their degree of biological realism and empirical support. These assumptions can have substantial impacts on the estimates produced by molecular dating analyses. The aim of this review is to open the ‘black box’ of Bayesian molecular dating and have a look at the machinery inside. We explain the components of these dating methods, the important decisions that researchers must make in their analyses, and the factors that need to be considered when interpreting results. We illustrate the effects that the choices of different models and priors can have on the outcome of the analysis, and suggest ways to explore these impacts. We describe some major research directions that may improve the reliability of Bayesian dating. The goal of our review is to help researchers to make informed choices when using Bayesian phylogenetic methods to estimate evolutionary rates and timescales.     

Key Innovations: Further Remarks on the Importance of Morphology in Elucidating Systematic Relationships and Adaptive Radiations

The present paper is an argument in support of the continued importance of morphological systematics and a plea for improving molecular phylogenetic analyses by addressing explicit character transformations. We use here the inference of key innovations and adaptive radiations to demonstrate why morphological systematics is still relevant and necessary. After establishing that theories of phylogenetic relationship offer robust explanatory bases for discussing evolutionary diversification, the following topics are addressed: (1) the inference of key innovations grounded in phylogenetic analyses; (2) the epistemic distinction between character ‘mapping’ and relevant evidence in systematic and evolutionary studies; and (3) key innovations in molecular phylogenetics. We emphasize that the discovery of key innovations, in fossil or extant taxa, further strengthens the importance of morphology in systematic and evolutionary inferences, as they reveal scenarios of character transformation that have led to asymmetrical sister-group diversification. Our main conclusion is that understanding characters in and of themselves, when properly contextualized systematically, is what evolutionary biologists should be concerned with, whereas the analysis of tree topology alone, in which statistical nodal support measures are the sole indicators of phylogenetic affinity, does not lead to a fuller understanding of key innovations.     

Phylogenetic networks: modeling, reconstructibility, and accuracy

Phylogenetic networks model the evolutionary history of sets of organisms when events such as hybrid speciation and horizontal gene transfer occur. In spite of their widely acknowledged importance in evolutionary biology, phylogenetic networks have so far been studied mostly for specific data sets. We present a general definition of phylogenetic networks in terms of directed acyclic graphs (DAGs) and a set of conditions. Further, we distinguish between model networks and reconstructible ones and characterize the effect of extinction and taxon sampling on the reconstructibility of the network. Simulation studies are a standard technique for assessing the performance of phylogenetic methods. A main step in such studies entails quantifying the topological error between the model and inferred phylogenies. While many measures of tree topological accuracy have been proposed, none exist for phylogenetic networks. Previously, we proposed the first such measure, which applied only to a restricted class of networks. In this paper, we extend that measure to apply to all networks, and prove that it is a metric on the space of phylogenetic networks. Our results allow for the systematic study of existing network methods, and for the design of new accurate ones.