Phylogenetic position of the acariform mites: sensitivity to homology assessment under total evidence

Background: Mites (Acari) have traditionally been treated as monophyletic, albeit composed of two major lineages: Acariformes and Parasitiformes. Yet recent studies based on morphology, molecular data, or combinations thereof, have increasingly drawn their monophyly into question. Furthermore, the usually basal (molecular) position of one or both mite lineages among the chelicerates is in conflict to their morphology, and to the widely accepted view that mites are close relatives of Ricinulei. Results: The phylogenetic position of the acariform mites is examined through employing SSU, partial LSU sequences, and morphology from 91 chelicerate extant terminals (forty Acariformes). In a static homology framework, molecular sequences were aligned using their secondary structure as guide, whereby regions of ambiguous alignment were discarded, and pre-aligned sequences analyzed under parsimony and different mixed models in a Bayesian inference. Parsimony and Bayesian analyses led to trees largely congruent concerning infraordinal, well-supported branches, but with low support for inter-ordinal relationships. An exception is Solifugae + Acariformes (P. P = 100%, J. = 0.91). In a dynamic homology framework, two analyses were run: a standard POY analysis and an analysis constrained by secondary structure. Both analyses led to largely congruent trees; supporting a (Palpigradi (Solifugae Acariformes)) clade and Ricinulei as sister group of Tetrapulmonata with the topology (Ricinulei (Amblypygi (Uropygi Araneae))). Combined analysis with two different morphological data matrices were run in order to evaluate the impact of constraining the analysis on the recovered topology when employing secondary structure as a guide for homology establishment. The constrained combined analysis yielded two topologies similar to the exclusively molecular analysis for both morphological matrices, except for the recovery of Pedipalpi instead of the (Uropygi Araneae) clade. The standard (direct optimization) POY analysis, however, led to the recovery of trees differing in the absence of the otherwise well-supported group Solifugae + Acariformes. Conclusions: Previous studies combining ribosomal sequences and morphology often recovered topologies similar to purely morphological analyses of Chelicerata. The apparent stability of certain clades not recovered here, like Haplocnemata and Acari, is regarded as a byproduct of the way the molecular homology was previously established using the instrumentalist approach implemented in POY. Constraining the analysis by a priori homology assessment is defended here as a way of maintaining the severity of the test when adding new data to the analysis. Although the strength of the method advocated here is keeping phylogenetic information from regions usually discarded in an exclusively static homology framework; it still has the inconvenience of being uninformative on the effect of alignment ambiguity on resampling methods of clade support estimation. Finally, putative morphological apomorphies of Solifugae + Acariformes are the reduction of the proximal cheliceral podomere, medial abutting of the leg coxae, loss of sperm nuclear membrane, and presence of differentiated germinative and secretory regions in the testis delivering their products into a common lumen.

This article is part of Almir R. Pepato's PhD thesis developed at the Universidade de São Paulo and supported by FAPESP (05/03458-1). High-performance cluster infrastructure was provided by the Molecular Systematic Laboratory at the Department of Zoology - IB/USP, financed by FAPESP (Proc. Nos. 2003/10335-8, 2004/09961-4, 2005/01299-3, and 2008/06604-7). Authors gratefully acknowledge Dr. Fernando Portella de Luna Marques (IBUSP) for the constant assistance concerning the analysis implementation. Special thanks are due to Dr. Karl Kjer (Rutgers University, New Jersey), Dr. Leandro Cézane de Souza Assis (IBUSP), Bsc. Maxmiliano Maronna (IBUSP), Dra. Grace Wyngaard (James Madison University, Harrisonburg), Dr. Gilberto José de Moraes (ESALQ-USP), Dr. Carlos Holger Wenzel Flechtmann (ESALQ-USP), and Dr. Márcio Bernardino da Silva (UFPB) for reading early drafts of this study and providing very useful suggestions on the study directions and to Dr. Eduardo Gorab (IBUSP) for suggestions on secondary structure issues. We also thank three anonymous referees for valuable comments on earlier versions of the manuscript.