Determination of paired fin or limb number, identity and position are key i
ssues in vertebrate development and evolution. Phylogenies including fossil
data show that paired appendages are unique to jawed vertebrates and their
immediate ancestry; that such fins evolved first as a single pair in an an
terior location; that appendicular endoskeletons are primitively AP asymmet
ric,, and that pectoral and pelvic fins primitively differ. It is conjectur
ed that Hox gene expression patterns along the lateral plate mesoderm estab
lish boundaries that contribute to localisation of AP levels at which signa
ls initiate outgrowth from the body wall. Such regionalisation may be regul
ated independently of that in the paraxial mesoderm and axial skeleton. Whe
n combined with current hypotheses of Hox gene phylogenetic and functional
diversity, these data suggest a new model of fin/limb developmental evoluti
on. This coordinates body wall outgrowth regions with primitive boundaries
established in the gut, and the fundamental non-equivalence of pectoral and
pelvic structures.