Arthropod phylogeny based on eight molecular loci and morphology

The interrelationships of major clades within the Arthropoda remain one of the most contentious issues in systematics, which has traditionally been the domain of morphologists1,2. A growing body of DNA sequences and other types of molecular data has revitalized study of arthropod phylogeny3,4,5,6,7 and has inspired new considerations of character evolution8,9. Novel hypotheses such as a crustacean–hexapod affinity4,10,11,12 were based on analyses of single or few genes and limited taxon sampling, but have received recent support from mitochondrial gene order13, and eye and brain ultrastructure and neurogenesis14,15. Here we assess relationships within Arthropoda based on a synthesis of all well sampled molecular loci together with a comprehensive data set of morphological, developmental, ultrastructural and gene-order characters. The molecular data include sequences of three nuclear ribosomal genes, three nuclear protein-coding genes, and two mitochondrial genes (one protein coding, one ribosomal). We devised new optimization procedures16,17 and constructed a parallel computer cluster with 256 central processing units18 to analyse molecular data on a scale not previously possible. The optimal ‘total evidence’ cladogram supports the crustacean–hexapod clade, recognizes pycnogonids as sister to other euarthropods, and indicates monophyly of Myriapoda and Mandibulata.