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The biogeography of Southeast Asia (SE Asia) is a good test ground in order to understand the effect of historical vicariant events on the contemporary patterns of species distribution. Earlier authors drew four biogeographic lines to explain the dissimilarities and similarities in the patterns of distribution of animals across the region. Later, Pleistocene "land-bridge" and geographic isolation theories were developed to explain genetic structuring among populations. More recently, areas of high endemicity have been suggested as potential rainforest refugia. The central question in this thesis is: What are the roles of geographic isolation and habitat differences in shaping fruit bat diversity at species and genetic levels? Field surveys were conducted in Sabah, Sarawak, Kalimantan, Peninsular Malaysia and Thailand. Diversity in the mtDNA cytochrome b gene was used to examine the relationships between current and historical population structure and ecological and morphological differences within Cynopterus brachyotis. The mtDNA cytochrome b phylogenetic reconstruction in the present study revealed of major division, with 100% bootstrap support, within C brachyotis. This phylogeny of Cynopterus species is discordant with both the classical hypothesis proposed by Andersen (1912) and present knowledge of fruit bat classification used by Corbet and Hill (1992), Wilson and Reeder (1993) and Schmitt et al. (1995). mtDNA sequence divergence is very high, about 9%-12% among the two major lineages of C. brachyoti. The two putative taxa found within C brachyotis populations were not sister taxa. There was correlation between the genetic lineages and the ecological habitats and morphological characteristics of these short-nosed fruit bats. C. brachyotis 1 (Cb 1) is morphologically larger and inhabits open habitats and C brachyotis 1 1 (Cb 11) is smaller and occurs in closed forest. The two lineages co-exist in forest edge habitats. The deep branch of Cb 1 suggests an older lineage compared to Cb 11. Cb 11, which is a derived form, is more closely related to its congencrics C. horsfieldi and C sphinx. which also occur in closed forests across the Sunda Shelf. These results indicate that the genetic divergence presently observed in C brachyotis populations is due to the presence of two, rather than one species. The widespread distribution and antiquity of C. brachyotis and the uncertain taxonomy of other members of the genus precludes any firm conclusions about the mechanisms of their speciation. However, tentative hypotheses are suggested, pending further molecular research using nuclear DNA.
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