ORGANIZATION into gene clusters is an essential and diagnostic feature
of Hox genes(1). Insect and nematode genomes possess single Hox gene
clusters (split in Dvosophila); in mammals, there are 38 Hox genes in
four clusters on different chromosomes(2,3). A collinear relationship
between chromosomal position, activation time and anterior expression
limit of vertebrate Hox genes suggests that clustering may be importan
t for precise spatiotemporal gene regulation and hence embryonic patte
rning(2,4). Hox genes have a wide phylogenetic distribution within the
metazoa, and are implicated in the control of regionalization along t
he anteroposterior body axis(2,5). It has been suggested that changes
in Hox gene number and genomic organization played a role in metazoan
body-plan evolution(6-8), but identifying significant changes is diffi
cult because Hox gene organization is known from only very few and wid
ely divergent taxa (principally insects, nematodes and vertebrates)(3)
. Here we analyse the complexity and organization of Hox genes in a ce
phalochordate, amphioxus, the taxon thought to be the sister group of
the vertebrates(9). We find that the amphioxus genome has only one Hox
gene cluster. It has similar genomic organization to the four mammali
an Hox clusters, and contains homologues of at least the first ten par
alogous groups of vertebrate Hox genes in a collinear array. Remarkabl
y, this organization is compatible with that inferred for a direct anc
estor of the vertebrates; we conclude; that amphioxus is a living repr
esentative of a critical intermediate stage in Hox cluster evolution.