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Eukaryotic cells, with complex features such as membrane-bound nuclei, evolved from prokaryotic cells that lack these components. A newly identified prokaryotic group reveals intermediate steps in eukaryotic-cell evolution. See Article p.353 Although the origin of eukaryotic cells from prokaryotic ancestors remains an enigma, it has become clear that the root of eukaryotes lies among a group of prokaryotes known as archaea. The recent identification of newly described archaea belonging to the Asgard superphylum, including Lokiarchaeota and Thorarchaeota, revealed a group of prokaryotes containing many proteins and genetic sequences that are otherwise found only in eukaryotes. Thijs Ettema and colleagues extend the search for eukaryotic roots by describing further additions to the Asgard superphylum: the Odinarchaeota and Heimdallarchaeota. The new Asgard genomes encode homologues of several components of eukaryotic membrane-trafficking machineries, suggesting that the archaeal ancestor of eukaryotes was well equipped to evolve the complex cellular features that are characteristic of eukaryotic cells.

The sequences of two sponge genomes provide evidence that the ParaHox developmental genes are older than previously thought. This has implications for animal taxonomy and for developmental and evolutionary biology. See Letter p.620 The simple body plan of sponges belies the complexity of their genomes, which contain a variety of transcription factors involved in body patterning in more complex creatures, such as Antennapedia class genes that in bilaterians (animals with distinct anterior and posterior ends) include Hox, ParaHox and NK. The genome of the demosponge Amphimedon queenslandica contains a tight cluster of NK genes, but no Hox or ParaHox genes. This led to the hypothesis that Hox and ParaHox genes evolved after sponges diverged from the lineage leading to cnidaria (jellyfishes, sea anemones and others) and bilateria. Study of the overall structure of the sponge genome suggested, however, that Hox and ParaHox might once have been present and later lost — the 'ghost locus' hypothesis. Maja Adamska and colleagues have studied the genome of two calcisponges, a distinct lineage from demosponges, and show that whereas the NK genes are not clustered, there is at least one ParaHox gene (Cdx). This adds weight to the ghost locus hypothesis and highlights the need to examine the genomes of many different sponge lineages in order to obtain a more complete picture of the ancestral animal complement of Antennapedia genes.