Copeia 2010, No. 3, 520–524 Promoting Resolution of the Percomorph Bush: A Reply to Mooi and Gill Wm. Leo Smith1 ‘‘If I’d asked . what they wanted, they’d have said a faster every test available to them at the primary homology stage, I horse.’’—Henry Ford, discussing innovation and the disagree with Mooi and Gill’s ever-present critique of building of his first automobiles character optimization. This stance gives the impression that they disregard or reject character congruence as the N their commentary, abstract, and presentation, Mooi final and decisive test of homology. Contrary to Mooi and and Gill (2008, 2010) sounded an alarm regarding what Gill (2010), we cannot ‘‘understand character homology’’ or I they perceive as an impending crisis in systematic justify special pleading for the uniqueness of characters; we ichthyology. This crisis is not impending; we are in the can only hypothesize that two entities are homologous midst of it. At higher levels, systematic ichthyology has been using all available evidence and let the totality of the data in in a stalemate for 35 years for percomorphs and for nearly a the analysis corroborate or refute the hypothesis of synapo- century for the ‘‘percoids’’ or moronoids. The alarm has morphy. To do anything else introduces unnecessary bias been going off for decades, and we are now just beginning to and assumptions. The difference between my view and the move beyond the crisis through the explicit analysis of view expressed by Mooi and Gill (2010) regarding the datasets aimed at resolving long-standing questions in importance of an explicit optimality criterion and character percomorph systematics (Springer and Orrell, 2004; Smith optimization is the core difference between the ‘‘trans- and Craig, 2007; Thacker, 2009). The phylogenetic hypoth- formed’’ and ‘‘numerical’’ phylogenetic schools (sensu eses and resulting changes to the classification recommend- Ebach et al., 2008). This conflict, I believe, exacerbates the ed by these studies are intriguing and have molecular and/or molecular vs. morphological data ‘‘rift’’ in systematic morphological support, but like all hypotheses, they ichthyology that Chakrabarty (2010) and Mooi and Gill demand further study. In the future, I hope that Mooi, Gill, (2010) discuss. Data chauvinism exists for both morpholog- and other researchers will examine the evidence for these ical and molecular systematists, so it would be most phylogenetic proposals or propose new evidence-based productive to focus the debate on the few fundamental relationships for other groups. As it stands, Mooi and Gill’s differences in the treatment, presentation, and analysis of (2010) critique is thoughtful, but it does not provide any data between the two phylogenetic schools rather than the counter-evidence for a single clade, recommendation, or class of data being studied. relationship proposed in the criticized studies; it just I have argued that our field’s lack of progress on higher- protests their existence. The percomorph bush will not level relationships, generally, and within percomorphs, resolve itself, and ichthyology will only make progress by specifically, is due to (1) our reliance on inexplicit analyses, incorporating new data and by performing explicit analyses. (2) dogmatic thinking about characters and relationships, The days of defending a 100-year-old taxonomic status quo and (3) analyzing insufficient data (as discussed in Smith that lacks evidence for its decisions are, thankfully, and Craig, 2007). In that study, we proposed novel numbered. relationships and a revised classification for the Percoidei, Mooi and Gill’s (2010) claim that the cause for the Epinephelidae, and Serranidae. These revisions were based impending crisis is ‘‘that the movement from synapomor- on a synapomorphy-rich parsimony hypothesis, which phy-based topologies to those based on statistical measures required a substantive break from the traditional percoid has removed the opportunity for rational discussion based classification handed down nearly 100 years ago from the on homology.’’ I agree with Mooi and Gill that homology likes of Regan (1913) and Jordan (1923). Mooi and Gill and synapomorphies are critical to phylogenetics, which is (2010) criticized our results (in non-specific terms) and the why every phylogeny that I have ever published is based conclusions of this and several other recent analyses that implicitly on synapomorphies; they are present for every have changed acanthomorph classification. Instead of recovered node. Further, I have always provided diagnostic discussing the three arguments put forward by Smith and features for every named clade (note that Moronoidei’s Craig (2007), Mooi and Gill (2010) focused their critique on stated usage was as a temporary grade, not a clade). Despite (1) ‘‘the clear trend in systematics towards a completely our agreement on the value of synapomorphy, Mooi and statistical and tree-based cladistics away from an evidence Gill’s (2010) assertion that ‘‘systematics is in danger of and character-based approach,’’ (2) ‘‘the apparent confusion making itself irrelevant to the remainder of biology because between homology, homoplasy, and the meaning of meaningful dialogue or assessment of synapomorphies has evidence,’’ and (3) ‘‘the impact of methods of analysis that become impossible’’ is hyperbole. The rise of comparative are, for all intents and purposes, phenetic.’’ Concerns 1 and methods (e.g., models of character evolution, diversification 3 are effectively redundant because a study that is phenetic analyses, biogeography) that have been developed via the would definitionally not be discretely character based, and if statistical framework of model-based analyses has only a study were phenetic, it would not make the distinction strengthened the influence of phylogenetics in biology. between homology and homoplasy (concern 2). In a sense, While I do agree with Mooi and Gill (2010) that researchers these concerns are a single criticism against numerical should take homology assessment seriously and make use of phylogenetics and character optimization: Mooi and Gill 1 The Field Museum, Department of Zoology, Fishes, 1400 South Lake Shore Drive, Chicago, Illinois 60605; E-mail: [email protected]. Submitted: 26 April 2010. Accepted: 24 May 2010. F 2010 by the American Society of Ichthyologists and Herpetologists DOI: 10.1643/OT-10-087c Comments 521 believe these methods are phenetic. The criticized studies state across all these groups in the primary homology use techniques that are not phenetic for several reasons. assessment stage. Even with this additional testing, it is First, phenetics relies on the analysis of a table of pairwise irresponsible for any systematist to assume that they can distances (a distance matrix) rather than the raw character fully ‘‘understand’’ a character system and bypass the test of matrix. Because of the reduction of the discrete character character congruence. matrix to pairwise distances, individual character changes Mooi and Gill (2010) never discuss character congruence (e.g., synapomorphies) cannot be optimized on the resulting as a test of homology except when they dismissively state, phenogram. In contrast, maximum likelihood, Bayesian, ‘‘optimization procedures are being relied upon to ‘solve’ and parsimony analyses are based on the analysis of the raw issues of homology rather than relying on biology.’’ As molecular sequence (character and character-state) data; this noted above, character congruence has always had an use of the discrete character data allows for the optimiza- important role in homology assessment (Patterson, 1982; tion/mapping/tracing of hypothesized transformations Rieppel and Kearney, 2007), and it is, after all, the final through ancestral states reconstruction (i.e., the identifica- arbiter of what character states are synapomorphies in a tion of synapomorphies). Second, likelihood, Bayesian, and given study. To suggest that relying on character congru- parsimony analyses use an explicit root to polarize all ence, or what is effectively the preponderance of the data or hypothesized transformations; this outgroup rooting results the weight of the evidence, is equivalent to ignoring in phylogenies that are informed solely by synapomorphy, homology goes against logic and the scientific method. not similarity. These methods are simply not phenetic. Mooi and Gill (2010) suggest, ‘‘a change in topology with Beyond this criticism, Mooi and Gill make additional claims the addition of taxa is an indication that there is no that demand address. Several of these issues will be discussed understanding of character homology.’’ This suggests that a below with the goal of promoting this discussion further, so systematist can know the Truth regarding all questions of that ichthyologists can once again focus on resolving the homology, homoplasy, convergence, and relationships prior phylogeny and taxonomy of fishes. to an analysis. Minimally, these types of assumptions about homology and monophyly (see Outgroup analysis below) Character congruence and molecular homology.—Mooi and will introduce bias into the analysis for all but the simplest Gill (2010) implore systematists to ‘‘return to homology,’’ of datasets. It is not possible to assess synapomorphy vs. and they suggest that ‘‘molecular data are really not convergence without explicit analyses, and all ichthyolo- substantively different from morphological data and should gists agree that homoplasy is rampant within Percomorpha.