1 <h5>Introduction</h5> The broad application of molecular techniques to phylogenetic reconstruction has revealed unrecognized levels of diversity in many vertebrate groups ( Gleeson et al., 1999 ; Kizirian and Cole, 1999 ; Roca et al., 2001 ). In bats, the recent identification of morphologically cryptic, genetically divergent species, even within well-studied genera ( Areletaz et al., 1997 ; Barratt et al., 1997 ; Kingston et al., 2001 ; Mayer and von Helversen, 2001 ; von Helversen et al., 2001 ), suggests that diversity within the order Chiroptera may be underestimated by current taxonomy. Likewise, the higher-level molecular systematics of Chiroptera have been the focus of numerous studies ( Simmons, 1998 ; Simmons and Geisler, 1998 ; Teeling et al., 2000 ; Van Den Bussche and Hoofer, 2001 ), yet many interspecific phylogenetic relationships remain poorly characterized, particularly in tropical regions where diversity is highest ( Jones et al., 2002 ). The distribution of the Old World fruit bat genus Cynopterus ( Fig. 1A ), spans more than 40° of latitude and 60° of longitude in the Indomalayan region, and encompasses the continental and oceanic islands of the Sunda shelf ( Fig. 1B ) and the western portion of
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