Four of the five tortoise species in Madagascar, Pyxis arachnoides, P. plan
icauda, Geochelone radiata, and G. yniphora, are endemic and on the verge o
f extinction, Their phylogenetic relationships remain controversial and unr
esolved. Here we address the phylogeny of this group using DNA sequences fo
r the 12S and 16S rDNA and cyt b genes in mitochondrial DNA. As outgroups w
e used two species of Geochelone, pardalis (mainland Africa) and nigra (Gal
apagos), as well as a more distant North American tortoise, Gopherus polyph
emus, We conclude that the two Pyxis species are sister taxa and are imbedd
ed in the genus Geochelone, rendering this latter genus paraphyletic. There
is moderate support for the sister status of the two Madagascar Geochelone
and for the monophyletic origin of all four endemics, suggesting a single
colonization of the island. The separation of Madagascar from other land ma
sses (90-165 mya) predates the origin of the endemic tortoises (estimated t
o be 14-22 mya), This suggests founding by rafting, a process known to have
occurred with other tortoises. The derived morphological divergence of the
Pyxis species in a relatively short period of time (13-20 my) stands in co
ntrast to the notoriously slow rate of morphological evolution in most line
ages of Chelonia. (C) 1999 Academic Press.