Arthropod phylogeny revisited, with a focus on crustacean relationships

Higher-level arthropod phylogenetics is an intensely active field of research, not least as a result of the hegemony of molecular data. However, not all areas of arthropod phylogenetics have so far received equal attention. The application of molecular data to infer a comprehensive phylogeny of Crustacea is still in its infancy, and several emerging results are conspicuously at odds with morphology-based studies. In this study, we present a series of molecular phylogenetic analyses of 88 arthropods, including 57 crustaceans, representing all the major lineages, with Onychophora and Tardigrada as outgroups. Our analyses are based on published and new sequences for two mitochondrial markers, 16S rDNA and cytochrome c oxidase subunit I (COI), and the nuclear ribosomal gene 18S rDNA. We designed our phylogenetic analyses to assess the effects of different strategies of sequence alignment, alignment masking, nucleotide coding, and model settings. Our comparisons show that alignment optimization of ribosomal markers based on secondary structure information can have a radical impact on phylogenetic reconstruction. Trees based on optimized alignments recover monophyletic Arthropoda (excluding Onychophora), Pancrustacea, Malacostraca, Insecta, Myriapoda and Chelicerata, while Maxillopoda and Hexapoda emerge as paraphyletic groups. Our results are unable to resolve the highest-level relationships within Arthropoda, and none of our trees supports the monophyly of Myriochelata or Mandibulata. We discuss our results in the context of both the methodological variations between different analyses, and of recently proposed phylogenetic hypotheses. This article offers a preliminary attempt to incorporate the large diversity of crustaceans into a single molecular phylogenetic analysis, assessing the robustness of phylogenetic relationships under varying analysis parameters. It throws into sharp relief the relative strengths and shortcomings of the combined molecular data for assessing this challenging phylogenetic problem, and thereby provides useful pointers for future studies.