Includes bibliographical references (leaves 78-88).The unique skeletal structure of the bat forelimb and hindlimb provides a new and exciting model for the field of evolutionary developmental biology, which seeks to reveal the molecular mechanisms behind vertebrate limb diversity. The digits of the bat forelimb, excluding the thumb, are considerably elongated and webbed. The hindlimb digits are free of webbing and are of uniform length, lacking the asymmetrical patterning of the forelimb. In this study, gene expression analysis has revealed that changes in the spatial and temporal expression patterns of the anteriorposterior patterning signal, Sonic hedgehog (Shh), and its downstream target, Patched 1 (PtcJ), have contributed to the development of the unique bat limb. The embryonic development of Miniopterus natalensis (Miniopteridae) is described for the first time and the expression patterns of Shh and PtcJ in the developing limbs of this species are compared to those in Carollia perspicillata (Phyllostomidae) and the mouse. Early in bat limb development (stage 14), Shh expression in the ZPA appears to be anteriorly expanded when compared to the mouse. This observation is in line with the reported expansion of Fgf8 expression in the AER (Cretekos et al. 2007) and reveals that an enhancement of the Shh-Fgf positive feedback loop may be responsible for the initial posterior expansion of the bat forelimb. Later in development (stage 16) Shh and PtcJ acquire a novel domain of expression within the interdigital tissue of both the bat forelimb and hindlimb. These expression patterns parallel the reported up-regulation of Fgf8, Gremlin and Bmp2 in the interdigital tissue of C. perspicillata (Weatherbee et al. 2006) and support the hypothesis that the Shh-Fgfpositive feedback loop is re-initiated in the interdigital tissue of the bat limbs. The cell survival and proliferation signals provided by the Shh-Fgf signalling loop most likely contribute to the lengthening of the posterior forelimb digits, the survival of the tissue between the forelimb digits and the extension of digits 1 and 5 of the hindlimb to the same length of the remaining digits. The novel Shh and PtcJ expression patterns were observed in both M natalensis and C. perspicillata, supporting the monophyly of the chiropteran sub-order, Verspertilioniformes
