An Analytical Approach Morphology, Shape and Phylogeny by Peter J. Wagn

Palaeontologia Electronica http://palaeo-electronica.org Fossils, Phylogeny, and Form: An Analytical Approach by Jonathan M. Adrain, Gregory D. Edgecombe, and Bruce S. Lieberman (editors) Topics in Geobiology vol. 19. Kluwer Academic / Plenum Publishers, New York, 2001, 402 p. ISBN: 0-306-46721-6. $130.00. Morphology, Shape and Phylogeny by Norman MacLeod and Peter Forey (editors) Systematics Association Special Volume no. 64. Taylor and Francis, London and New York, 2002, 308 p. ISBN: 0-415-24074-3. £70.00/$125.00 by Peter J. Wagner In the eleven conference of the years since Harvey Systematics Associa- and Pagel (1991), tion with the same evolutionary biolo- name as the book. gists committed con- This excellent volume siderable includes papers deal- methodological effort ing with both aspects into the relationship of morphometric data between phylogeny and phylogeny: how and numerous types one can infer phylog- of patterns. Morphol- enies or even test ogy, Shape and Phylogeny and Fossils, phylogenetic hypotheses from morpho- Phylogeny, and Form both concern metric data, and how one can reconstruct themselves with these issues. The former continuous character evolution over model book deals primarily with the relationship phylogenies. Of course, these concepts between phylogeny and continuous mor- are inexorably linked and several of the phometric data, whereas the latter deals papers treat both issues. The authors with a variety of other issues also. include many of the movers and shakers MacLeod and Forey's text stems from of morphometric, phylogenetic and tree- the 1999 Second Biennial International based methodology. Whether continuous Wagner, Peter J., 2003. FOSSILS, PHYLOGENY, AND FORM: AN ANALYTICAL APPROACH and MORPHOLOGY, SHAPE AND PHYLOGENY. Palaeontologia Electronica, vol. 5, issue 2, book review 3: 15pp., 170KB; http://palaeo-electronica.org. WAGNER, PETER J.: FOSSILS, PHYLOGENY, AND FORM: AN ANALYTICAL APPROACH MORPHOLOGY, SHAPE AND PHYLOGENY data contribute to phylogenetic studies Felsenstein also notes that the mathemati- (one of contention not long ago) receives cal intractability of juggling so many little attention - the authors unanimously parameters means that we will have to use agree that continuous characters can do Markov Chain Monte Carlo (MCMC) meth- so. The closest thing to a dissenting voice ods (e.g., Larget and Simon 1999) to find is Humphries' short paper, and even he and "integrate" over likely parameter val- backs off from his previous stand (e.g., ues. (Notably, Felsenstein does not com- Cranston and Humphries 1988) and con- ment on using MCMC to estimate cludes that any type of data is suitable for Bayesian probabilities of parameters.) phylogenetic study. Humphries does Other papers focus on recognizing lament that ideas about transformation states within continuous characters. Rae's and character evolution have become chapter is concerned (in large part) with muddle with the concepts of sorting the correlation between size and shape homologies and classification. However, and how that affects residuals and cen- one thing made clear by many of the troids. However, as I note above, corre- papers in the volumes is that the former lated change is a potential problem for all concept is inseparable from the two ideas. character data (including molecular data). (The relationship of classification to any of Rae advocates the use of ratios, but I am this is arbitrary philosophy, of course.) skeptical of such approaches simply Two distinct concepts accompany because there are numerous transforma- reconstructing phylogeny from morpho- tions than can result in similar ratios metric data - estimating phylogeny directly among features, and because many fea- from morphometric data, and inferring tures that one might describe with ratios characters and character states from mor- will themselves not be independently phometric data. Given the choices of qual- evolving ones. Reid and Sidwell summa- ifying continuous data or analyzing it rize methods commonly used to divide directly, Felsenstein opts for the latter. As continua into discrete characters and note he warns, it will not be easy. Of particular that all suffer from problems. As Felsen- importance here are the effects of corre- stein notes, variation in peak conditions lated change. This is critical when examin- among closely related species would blur ing multiple landmarks associated with the boundaries even if state transformations same homology, but really represents an were fairly discrete, so perhaps these under-addressed problem that is not problems should not be surprising. unique to morphometric data (e.g., Perhaps the most interesting papers in McCracken et al. 1999.) He also briefly this section are the ones dealing with geo- outlines the role of fossils in such analy- metric morphometric methods for inferring ses, noting two ways in which they can be characters and states. Chapters by Swid- handled: using model molecular trees to erski, Zelditch and Fink and by MacLeod estimate covariance and rate patterns offer interesting points and counterpoints among landmarks, and then assigning fos- concerning landmark versus outline analy- sils to their most likely positions, or trying ses. Swiderski et al. continue earlier to simultaneously estimate (or test) mor- papers (e.g., Zelditch et al. 1995; Swider- phological parameters and phylogenetics ski et al. 1998) exploring how one might topology. (Although Felsenstein does not use Bookstein's thin-plate splines methods mention it, this is the only option when to infer characters. In particular, they dealing with completely extinct taxa.) examine partial warps, which are analo- 2 WAGNER, PETER J.: FOSSILS, PHYLOGENY, AND FORM: AN ANALYTICAL APPROACH MORPHOLOGY, SHAPE AND PHYLOGENY gous to Factor Analysis scores, with the and larger samples might have relative eigenvectors (principal warps) derived warps confounded by phylogenetics auto- from a description of non-uniform differ- correlation. Although MacLeod dismisses ences between observed forms and some Swiderski et al.'s criticism of using multi- reference form. The authors repeat some variate summaries of distributions to infer of their concerns about using "traditional" characters and states, eigenvectors might methods (e.g., principal components anal- blend multiple warps diagnosing particular ysis) to identify multivariate characters on clades, and distort warps that change the grounds that phylogenetic autocorrela- occur with numerous combinations of tion has strong effects on the relative other warps. Similarly, eigenshape analy- importance of eigenvectors. Also ses (which use eigenvectors derived from (although the authors do not state this angular differences between specimen explicitly), phylogenetic autocorrelation will outlines and some standard outline) run a cause eigenvectors to summarize suites of similar risk of blurring/distorting indepen- states separating clades and paraclades, dent derivations because phylogeny can- and thus can miss biologically indepen- not be removed. Still, eigenshape dent features. More notably, the authors analyses are able to replicate (and back away from some of their previous improve upon) nominal characters and positions. For example, they do not rec- states for trilobite pygidia. Given the pau- ommend using partial warps as a means city of character states for trilobites (and, of exploring for characters rather than to a lesser extent, other commonly fossil- diagnosing them. They also acknowledge ized taxa), this is at least a start. For their that outline methods are needed to part, Swiderski et al. offer measures such describe differences in shapes between as smoothness, sinuosity, etc. as possible homologous landmarks. MacLeod illus- measures of outline shapes rather than trates some of the weaknesses of partial multivariate reductions such as eigen- warps using empirical and simulated shape axes. However, this will reintroduce examples. Unfortunately, the empirical tri- the problem of categorizing continua into lobite example is not a good test case - tri- discrete characters if one is to use such lobite matrices (including the one used by features as character states. MacLeod) have notoriously poor resolu- Bookstein offers a different take on tion of states (Wagner 2000b) and the dis- identifying character states, summarizing agreement between partial warps and his creases technique. A "crease" is the nominal characters might be telling us apex of a function in morphospace more about the inadequacy of the nominal describing an axis of deformation between characters than of partial warps. However, two types and thus the transition boundary the inability of partial warps to replicate between two states. Visually, this is the known transformation patterns in simula- point where a D'Arcy Thomson-esque grid tions is damning. MacLeod advocates shows directly abutting curves at some using relative warps, i.e., the eigenvector extrapolation angle. Although the concept summaries of multivariate distributions is a little hairy, Bookstein offers a simple among partial warps. This does separate exercise involving basic geometric fea- out state types among simulated fish tures that illustrate it nicely. Bookstein pre- nicely, especially when the analyses are sents three empirical examples, two confined to particular organ systems. involving intraspecific variation (schizo- However, this is only a 10-taxon example phrenic vs. non-schizophrenic and male 3 WAGNER, PETER J.: FOSSILS, PHYLOGENY, AND FORM:

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