A new view of insectecrustacean relationships II. Inferences from expressed sequence tags and comparisons with neural cladistics David R. Andrew * Department of Neuroscience, University of Arizona,1040 E. 4th St., Gould-Simpson Bldg. #611, Tucson, AZ 85721, USA article info Article history: Received 3 September 2010 Accepted 1 February 2011 Keywords: Expressed sequence tag Phylogeny Arthropoda Tetraconata Pancrustacea Branchiopoda Hexapoda Nervous system evolution abstract The enormous diversity of Arthropoda has complicated attempts by systematists to deduce the history of this group in terms of phylogenetic relationships and phenotypic change. Traditional hypotheses regarding the relationships of the major arthropod groups (Chelicerata, Myriapoda, Crustacea, and Hexapoda) focus on suites of morphological characters, whereas phylogenomics relies on large amounts of molecular sequence data to infer evolutionary relationships. The present discussion is based on expressed sequence tags (ESTs) that provide large numbers of short molecular sequences and so provide an abundant source of sequence data for phylogenetic inference. This study presents well-supported phylogenies of diverse arthropod and metazoan outgroup taxa obtained from publicly-available data- bases. An in-house bioinformatics pipeline has been used to compile and align conserved orthologs from each taxon for maximum likelihood inferences. This approach resolves many currently accepted hypotheses regarding internal relationships between the major groups of Arthropoda, including monophyletic Hexapoda, Tetraconata (Crustacea þ Hexapoda), Myriapoda, and Chelicerata sensu lato (Pycnogonida þ Euchelicerata). “Crustacea” is a paraphyletic group with some taxa more closely related to the monophyletic Hexapoda. These results support studies that have utilized more restricted EST data for phylogenetic inference, yet they differ in important regards from recently published phylogenies employing nuclear protein-coding sequences. The present results do not, however, depart from other phylogenies that resolve Branchiopoda as the crustacean sister group of Hexapoda. Like other molecular phylogenies, EST-derived phylogenies alone are unable to resolve morphological convergences or evolved reversals and thus omit what may be crucial events in the history of life. For example, molecular data are unable to resolve whether a HexapodeBranchiopod sister relationship infers a branchiopod-like ancestry of the Hexapoda, or whether this assemblage originates from a malacostracan-like ancestor, with the morphologically simpler Branchiopoda being highly derived. Whereas this study supports many internal arthropod relationships obtained by other sources of molecular data, other approaches are required to resolve such evolutionary scenarios. The approach presented here turns out to be essential: integrating results of molecular phylogenetics and neural cladistics to infer that Branchiopoda evolved simplification from a more elaborate ancestor. Whereas the phenomenon of evolved simplification may be widespread, it is largely invisible to molecular techniques unless these are performed in conjunction with morphology-based strategies. Ó 2011 Elsevier Ltd. All rights reserved. 1. Introduction The enormous ecological, behavioral, and morphological diver- sity of Arthropoda has complicated attempts by systematists to resolve the evolutionary history of this species-rich and ancient group (Budd and Telford, 2009; Edgecombe, 2010). Support for nearly every possible relationship between the four major arthropod lineages has historically hallmarked research (for example, see Fig.1 in Strausfeld and Andrew, 2011); moreover, various sister group relationships of Arthropoda with Tardigrada and/or Onychophora (which with arthropods are referred to as Panarthropoda (Telford et al., 2008)) have been supported. However, a modern consensus is unfolding that confirms a monophyletic Arthropoda, compri- sing monophyletic Chelicerata, Myriapoda, and Tetraconata (Crustacea þ Hexapoda, the name based on the shared organization of crystalline cone cells of the ommatidia, Dohle, 1997, 2001; also called Pancrustacea, Zrzavy and Stys, 1997)(Roeding et al., 2007, 2009; Regier et al., 2008, 2010; Aleshin et al., 2009; Meusemann * Tel.: þ1 520 621 9668; fax: þ1 520 621 8282. E-mail address: dandrew@email.arizona.edu. Contents lists available at ScienceDirect Arthropod Structure & Development journal homepage: www.elsevier.com/locate/asd 1467-8039/$ e see front matter Ó 2011 Elsevier Ltd. All rights reserved. doi:10.1016/j.asd.2011.02.001 Arthropod Structure & Development 40 (2011) 289e302