Ancient homeobox gene loss and the evolution of chordate brain and pharynx development: deductions from amphioxus gene expression

Homeobox genes encode a large superclass of transcription factors with widespread roles in animal development. Within chordates there are over 100 homeobox genes in the invertebrate cephalochordate amphioxus and over 200 in humans. Set against this general trend of increasing gene number in vertebrate evolution, some ancient homeobox genes that were present in the last common ancestor of chordates have been lost from vertebrates. Here, we describe the embryonic expression of four amphioxus descendants of these genes—AmphiNedxa, AmphiNedxb, AmphiMsxlx and AmphiNKx7. All four genes are expressed with a striking asymmetry about the left–right axis in the pharyngeal region of neurula embryos, mirroring the pronounced asymmetry of amphioxus embryogenesis. AmphiMsxlx and AmphiNKx7 are also transiently expressed in an anterior neural tube region destined to become the cerebral vesicle. These findings suggest significant rewiring of developmental gene regulatory networks occurred during chordate evolution, coincident with homeobox gene loss. We propose that loss of otherwise widely conserved genes is possible when these genes function in a confined role in development that is subsequently lost or significantly modified during evolution. In the case of these homeobox genes, we propose that this has occurred in relation to the evolution of the chordate pharynx and brain

The impact of fossil data on annelid phylogeny inferred from discrete morphological characters

As a result of their plastic body plan, the relationships of the annelid wormsand even the taxonomic makeup of the phylum have long been contentious.Morphological cladistic analyses have typically recovered a monophyleticPolychaeta, with the simple-bodied forms assigned to an early-divergingclade or grade. This is in stark contrast to molecular trees, in which polychaetesare paraphyletic and include clitellates, echiurans and sipunculans.Cambrian stem group annelid body fossils are complex-bodied polychaetesthat possess well-developed parapodia and paired head appendages( palps), suggesting that the root of annelids is misplaced in morphologicaltrees. We present a reinvestigation of the morphology of key fossil taxaand include them in a comprehensive phylogenetic analysis of annelids.Analyses using probabilistic methods and both equal- and implied-weightsparsimony recover paraphyletic polychaetes and support the conclusion thatechiurans and clitellates are derived polychaetes. Morphological treesincluding fossils depict two main clades of crown-group annelids that aresimilar, but not identical, to Errantia and Sedentaria, the fundamentalgroupings in transcriptomic analyses. Removing fossils yields trees thatare often less resolved and/or root the tree in greater conflict with moleculartopologies. While there are many topological similarities between the analysesherein and recent phylogenomic hypotheses, differences include theexclusion of Sipuncula from Annelida and the taxa forming the deepestcrown-group divergences