Phylogenetic analysis of arthropods using two nuclear protein-encoding genes supports a crustacean plus hexapod clade

Recent phylogenetic analyses using molecular data suggest that hexapods are more closely related to crustaceans than to myriapods, a result that confl icts with long-held morphology-based hypotheses. Here we contribute additio nal information to this debate by conducting phylogenetic analyses on two n uclear protein-encoding genes, elongation factor-1 alpha (EF-1 alpha) and t he largest subunit of RNA polymerase II (Pol II), from an extensive sample of arthropod taxa. Results were obtained from two data sets. One data set c omprised 1092 nucleotides (364 amino acids) of EF-1 alpha and 372 nucleotid es (124 amino acids) of Pol II from 30 arthropods and three lobopods. The o ther data set contained the same EF-1 alpha fragment and an expanded 1038-n ucleotide (346-amino-acid) sample of Pol II from 17 arthropod taxa. Results from maximum-parsimony and maximum-likelihood analyses strongly supported the existence of a Crustacea + Hexapoda clade (Pancrustacea) over a Myriapo da + Hexapoda clade (Atelocerata). The apparent incompatibility between the molecule-based Pancrustacea hypothesis and morphology-based Atelocerata hy pothesis is discussed.