Review

Better shoes alone don’t get you to your destination

Reviewed by 1 RAFAEL MEDINA BERNARD GOFFINET Department of Ecology and Evolutionary Biology, 75 North Eagleville Road, University of Connecticut, Storrs, CT 06269-3043, U.S.A. 1e-mail: [email protected]

Zander, R. H. 2013. A Framework for Post-Phylogenetic Systematics. Zetetic Publications, St. Louis, MO 209 p. [ISBN 978-1492220404]. Price $ 19.98 (softcover).

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A major challenge of reconstructing evolutionary rela- work is summarized (Chapter 16). The book includes a tionships is how to deal with distinct branching orders in glossary, which is essential given that the author uses trees inferred from different datasets, in particular terms likely to be unfamiliar to most readers (self-nesting morphological and molecular datasets. Topological in- ladder, caulistic taxa, extended paraphyly, etc.). congruences should be fully reconcilable since these The most important criticism expressed by Zander, characters are drawn from the same organisms and hence and somehow his principal motivation, is phylogenetic should reflect the outcome of the same underlying structuralism, the belief that evolutionary patterns are macroevolutionary process. Current widely applied best described in terms of the properties and rules of fundamental theoretical principles severely constrain scientific constructs, specifically Hennigian cladograms. the interpretation of phylogenetic trees and constitute The cladistic logic for phylogenetic reconstruction perhaps the primary, most significant obstacle to unifying in terms of dichotomous sister-group relationships is inferences in an integrative evolutionary reconstruction. A commonly accepted as the legitimate way to represent critical evaluation of the applicability of these principles to the diversification of lineages through time, yet may in reflect natural processes has become necessary, consider- fact, on theoretical grounds alone, fail to reflect ing that large data sets are generated with relative ease, and evolutionary processes. To consider that internal nodes that topological conflict is likely to become the norm of a tree mark ancestors that are merely hypothetical, rather than the exception. Richard Zander, in his book A implies that speciation events are linked to the extinction Framework for Post-Phylogenetic Systematics,remindsus of the ancestral species (i.e., ‘‘pseudoextinction’’ in the that data and trees do not speak for themselves, and that it framework’s vocabulary). However, such assumption is we who provide the words to model the story about the seems to be only a formal convention that does not evolution of organisms. He challenges us to reflect on the match actual cases of speciation, where a ‘‘mother assumptions and constraints we have, often subcon- species’’ may remain virtually unchanged and paraphy- sciously, adopted. He outlines a new framework and, with letic after a budding speciation event. The consequences a provocative style, engages us in evaluating the principles of this assumption are extensively explored throughout we apply to the interpretation of trees inferred from data. Zander’s work, consequences that are unexpected and Zander starts with an analysis and critique of some of counterintuitive for those accustomed to think strictly in the widely applied methods of phylogenetics (Chapters 1 cladistic terms. Ultimately, a phylogenetic tree is still a and 2), setting the stage for the presentation of an graph that needs to be interpreted, a tool for evolution- innovative method for macroevolutionary reconstruction ary reconstruction, but not an evolutionary history itself. (Chapter 3), consisting of six fundamental ‘‘elements,’’ Similarly, incongruence between topologies inferred developed sequentially in Chapters 4–9. Further discus- from distinct data sets, in particular morphological and sion of aspects of systematic theory and method, such as molecular, should not be seen as hard incompatibilities the estimation of statistical support or the role of intuitive but rather ‘‘soft’’ incongruences as trees can potentially hypotheses (Chapters 10–15), follow before the frame- be reconciled given the proper interpretation.

The Bryologist 117(4), pp. 431–433 Published online: November 11, 2014 0007-2745/14/$0.45/0 432 THE BRYOLOGIST 117(4): 2014

Another issue that receives special attention is the cladistic constraints on the interpretation and recon- need to recognize and formalize classical taxonomy, struction of evolutionary phenomena. If heterophylly which is based on comparative morphology, as a reliable may be an artifact resulting from Hennigian constraints source of scientific knowledge. The value of this on our interpretation of trees, then it is imperative to approach is typically downgraded on the implicit consider alternative processes underlying a given tree or argument that classical taxonomy is impregnated with set of trees that do not rely on pseudoextinction, and the subjective appreciation of traits by the expert. In hence explore the effect of recognizing persistent comparison, current phylogenetic methods based on ancestral taxa (i.e., named internal nodes) on the molecular data seem more robust and sophisticated, so reconstruction of the evolutionary history. We also find that in cases of topological incongruence, inferences very valuable the discussion on the scientific legitimacy from molecular data are systematically preferred, with of classical taxonomy and the search of a formalization the consequences that homology assumptions of mor- of abductive reasoning. No doubt, this book will phological characters are more readily rejected. Zander stimulate readers familiar with current phylogenetics argues that classical morphological analysis is, however, a to evaluate the foundations that are often implicitly, refined methodology based on abductive reasoning and unconditionally or subconsciously followed. usually subconscious heuristics that should generate On the other hand, we find that the argumentation robust working hypotheses. The lack of a formalized presented to highlight the value of morphological system- mathematical expression or statistical support may atics and, in fact, its imperative inclusion in modern account for the perception of classical taxonomy as systematics (a point we agree with), is constantly incompatible with the ‘‘hard sciences,’’ but as Zander impregnated with an excessive mistrust of molecular reminds us, molecular data are not free of homoplasy phylogenetics. Zander’s main concern is that the modus either, may yield ambiguous signal also, and typically operandi of most modern systematists faced with topolog- suffer from limited sampling of conspecific exemplars. ical incongruence between morphology and molecule Furthermore, and perhaps most importantly and indeed based trees is to force the interpretation of the evolution often acknowledged, gene trees may not be reliable of morphological traits onto the molecular topology, and proxies of macroevolutionary (species) trees, and should hence to readily accept homoplasy in the morphological be regarded primarily as a graphic depiction of the traits, or to merge morphologically distinct lineages on the properties of a dataset, rather than of the evolutionary basis of recognizing only monophyletic lineages. Zander’s process directly. framework, however, is not free of a similar bias, since it With the aim of integrating the valuable sources of allows one to explain virtually all incongruences between information provided by classical taxonomy and molec- classical taxonomy and molecular trees in terms of artifacts ular phylogenetics, Zander proposes a method (the caused by cladistic structuralism, forcing the interpretation ‘‘framework’’ itself) consisting of the following steps: a of the molecular tree onto that inferred from morpholog- taxonomic treatment based on morphological analysis, ical traits (as if it were itself always an unequivocal exercise). followed by the generation of a natural key based on the We agree with the call for a pluralistic systematics, but do morphological treatment, then the incorporation of not endorse the approach to build evolutionary recon- molecular systematics analyses, and finally the optimi- struction on the immutable foundation provided by the zation and consolidation of both sources of information expert taxonomist. (including incipient mechanisms to integrate support Of course, the accumulated study of specimens values combining posterior probabilities and coarse leading to the elaboration of species concepts and priors). The goal is to reach a representation of the relationships is essential to the modern systematic evolutionary process that is not constrained by cladistic endeavor, but regardless of the time devoted to alpha structuralism, combines evidence from different sources taxonomy or the experience of the taxonomic authority, and allows for the recognition of paraphyletic taxa. As species concepts and relationships are only hypotheses. part of his framework, Zander proposes alternatives to The strength of these is highly dependent on the the traditional cladogram, to the Newick formula, and underlying assumptions one makes, and (here we agree the artificial dichotomous key, to integrate and reflect with Zander) one should be aware and remember these the processes that shape evolutionary histories. and assess their basis before endorsing or rejecting any The concerns expressed by Zander are not new—as one hypothesis. It is not pluralism to force all future reflected in his extensive bibliography, including his own contributions from molecular inferences to strengthen papers on phylogenetic methodology—but they are the concepts developed by expert taxonomists. Very nevertheless often overlooked. Perhaps many biologists often, the reader may find this book more a reaction have not even heard of these concerns. We agree that it is against the current preeminence of molecular systematics essential to keep in mind the limitations imposed by the than a balanced attempt to reconcile datasets of different Review 433 sources. The author, for instance, could acknowledge the family level derived from a putatively ancestral that the primary and perhaps even the main evidence Pottiaceae, even if deeply nested within the latter. The against a strictly monophyletic taxon concept is drawn problem, of course, comes with the perception of discon- from inferences from molecular data sampled for a larger tinuity. When should species be accommodated in their number of conspecific exemplars. genus, or genera in their distinct family? Is anything gained Zander urges the reader to integrate into the by recognizing the Ephemeraceae that is not reflected by evolutionary interpretation of trees the complexity of accepting Ephemerum as a distinct genus in the Pottiaceae? diagnostic traits, and the eco-geographic distributions of As is usually the case with works dealing with the species. Of course, homoplasy of complex traits may be nature of phylogeny and classification, this book is not unlikely, but to unconditionally assume homology of light reading. It engages the reader in stimulating and ‘‘complex’’ traits across the tree may also severely bias enjoyable discussions, often framed in a broader context interpretations and should thus be avoided, especially in of scientific methodology and epistemology. The reading the absence of actual knowledge of what constitutes the is, however, challenging and would have benefited from a complexity of a trait. Similarly, taxa with a broad more strategized structure. An explicit, even theoretical geographic and ecological distribution are assumed to scenario of budding evolution in the introduction would represent ancestral species. Although this may be intui- have prepared the reader more effectively for the tively appealing, it negates the possibility of specialists intellectual journey he was about to embark on. A less giving rise to generalists, or of taxa substantially expanding impulsive style, a more critical proofreading, and a their geographic ranges over short and recent periods of trimming of supernumerous words would also have eased geological time. Here the author fails to advocate or even the reading. The integration integration of more explicit suggest with the same vehemence, as when challenging us figures would have enhanced and strengthened the to broaden our interpretation of topological heterophyly, understanding of the arguments being developed. Certain the need to explore the effect of these assumptions on the recent papers by Zander (2014a,b,c) deal with the same interpretation and reconstruction of evolutionary history. issues in a more structured way with improved figures. A central issue in the book is the development of a Are we closer to a Kuhnian revolution transcending classification from phylogenetic trees, with a case made to current phylogenetics, as may be suggested by the title? It accept not just paraphyletic species but also paraphyletic is probably premature to go that far, and while doubt genera and families. It seems that the (sometimes intense) and critical re-examination of what is generally assumed debate on the recognition of paraphyletic taxa has become can be challenging, it is also stimulating and refreshing. more relaxed in recent years. Today, many systematists agree We would encourage any biologist seeking to unravel on the recognition of paraphyletic species (a dispersal to an evolutionary histories from morphological and molecu- oceanicislandfollowedbyasignificantdivergenceofthe lar data to pick up a copy of this book, engage in a resulting population does not mean that the ancestral reading unbiased by priors, consider possibilities to truly continental species has changed or become extinct), and integrate inferences from these data, and thereby explore perhapswecouldagreeonparaphylyalittleabovethe more critically their plausible interpretations. As the nominal species level, but as we climb to higher ranks, the generation of data becomes less the limiting factor to our argumentsbecomeincreasingly subjective. The discussion ability to reconstruct phylogenetic trees, we must reflect on the retention of paraphyletic supraspecific taxa rests on more on what those trees may reveal. the argument for maintaining the taxon that creates the paraphyly, and this argument seems biased by Zander’s LITERATURE CITED perceived notion of what constitutes important evolutionary Zander R. H. 2014a. Classical determination of monophyly, exemplified change. In this context, Zander highlights the synonymy of with Didymodon s.lat. (Bryophyta). Part 1 of 3, synopsis and simplified the Ephemeraceae (a family composed of one genus of concepts. Phytoneuron 78: 1–7. highly reduced ephemeral mosses) with the Pottiaceae (a Zander R. H. 2014b. Classical determination of monophyly, exemplified highly diverse lineage exhibiting broad amplitude of with Didymodon s.lat. (Bryophyta). Part 2 of 3, concepts. Phytoneuron 79: 1–23. morphological complexity, including some taxa of short- Zander R. H. 2014c. Classical determination of monophyly, exemplified lived plants). He implicitly argues that Ephemeraceae is with Didymodon s.lat. (Bryophyta). Part 3 of 3, analysis. Phytoneuron macroevolutionarily important and should be recognized at 80: 1–9.