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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\u2014<jats:italic>AmphiNedxa, AmphiNedxb, AmphiMsxlx<\/jats:italic>and<jats:italic>AmphiNKx7<\/jats:italic>. All four genes are expressed with a striking asymmetry about the left\u2013right axis in the pharyngeal region of neurula embryos, mirroring the pronounced asymmetry of amphioxus embryogenesis.<jats:italic>AmphiMsxlx<\/jats:italic>and<jats:italic>AmphiNKx7<\/jats:italic>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.<\/jats:p>","DOI":"10.1098\/rspb.2010.0647","type":"journal-article","created":{"date-parts":[[2010,6,17]],"date-time":"2010-06-17T00:20:07Z","timestamp":1276734007000},"page":"3381-3389","update-policy":"https:\/\/doi.org\/10.1098\/crossmark-policy","source":"Crossref","is-referenced-by-count":10,"title":["Ancient homeobox gene loss and the evolution of chordate brain and pharynx development: deductions from amphioxus gene expression"],"prefix":"10.1098","volume":"277","author":[{"given":"Thomas","family":"Butts","sequence":"first","affiliation":[{"name":"Department of Zoology, University of Oxford, South Parks Road, Oxford OX1 3PS, UK"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Peter W. 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