To test the validity of intron-exon structure as a phylogenetic marker, the
intron-exon structure of EF-1 alpha genes was investigated for starfish, a
cornworms. ascidians. larvaceans, and amphioxus and compared with that of v
ertebrates. Of the 11 distinct intron insertion sites found within the codi
ng regions of the deuterostome EF-lat genes, 7 are shared by several taxa,
while the remainder are unique to certain taxa. Examination of the shared i
ntrons of the deuterostome EF-1 alpha gene revealed that independent intron
loss or intron insertion must have occurred in separate lineages of the de
uterostome taxa. Maximum parsimony analysis of the intron-exon data matrix
recovered five parsimonious trees (consistency index = 0.867). From this re
sult, we concluded that the intron-exon structure of deuterostome EF-1 alph
a has evolved more dynamically than previously thought, rendering it unsuit
able as a phylogenetic marker. We also reconstructed an evolutionary histor
y of intron insertion-deletion events on the deuterostome phylogeny, based
on several molecular phylogenetic studies. These analyses revealed that the
deuterostome EF-1 alpha gene has lost individual introns more frequently t
han all introns simultaneously.