Abstract

Phylogenomic analyses have revealed several important metazoan clades, such as the Ecdysozoa and the Lophotrochozoa. However, the phylogenetic positions of a few taxa, such as ctenophores, chaetognaths, acoelomorphs, and Xenoturbella, remain contentious. Thus, the findings of qualitative markers or ‘‘rare genomic changes’ ’ seem ideal to independently test previous phylogenetic hypotheses. We here describe a rare genomic change, the presence of the gene UDP-GlcNAc 2-epimerase/N-acetylmannosamine kinase (GNE). We show that GNE is encoded in the genomes of deuterostomes, acoelomorphs and Xenoturbella, whereas it is absent in protostomes and nonbilaterians. Moreover, the GNE has a complex evolutionary origin involving unique lateral gene transfer events and/or extensive hidden paralogy for each protein domain. However, rather than using GNE as a phylogenetic character, we argue that rare genomic changes such as the one presented here should be used with caution. Key words: molecular markers, metazoan phylogeny, lateral gene transfer, Xenoturbella, UDP-GlcNAc 2-epimerase/N-acetylmannosamine kinase, acoels. Molecular signatures that characterize a clade are an important tool to create or corroborate phylogenetic groupings (reviewed in Telford and Copley 2011). Examples