The anuran fauna has been found to harbor substantial cryptic diversity, and chronic, low-level population declines in evolutionarily significant units can be masked by a lack of resolution on this diversity. Numerous species previously believed to be common and widespread have been found to represent cryptic species complexes consisting of distinct genetic lineages with restricted ranges. Most research on cryptic diversity has focused on high elevation areas because they usually harbor higher diversity and levels of endemism; thus cryptic diversity from lowland areas remains poorly understood. This study investigated the population divergence of the pearly-skinned floating frog (Occidozyga lima), a lowland wetland species broadly distributed throughout Southeast Asia and considered common throughout its range. I analyzed six DNA regions (Histone H3, Tyrosinase exon-1, 28S, 16S, ND1 and 12S; a total of 4,650 base pairs) to reconstruct the phylogenetic relationships among populations. Morphometric analyses were conducted to test for morphological differentiation. Both genetic and morphological data revealed substantial lineage divergence in O. lima. I found that sympatric lineages are not sister lineages, a common feature of cryptic species complexes. The current status of O. lima as a single species should be rejected. Three candidate species were delineated based on 5% mitochondrial 16S genetic divergence. The name O. lima should be restricted to populations in the type locality, Java, Indonesia (candidate species I), and two new species should be assigned to populations from South China to Northern Indochina (candidate species II) and Southern Indochina to Myanmar (candidate species III). Resolving the widely-distributed species complex into three valid species requires reassessment of the IUCN conservation status. Given observed population declines in South China and Indonesia, the new species are likely to belong to a higher threat category. Species considered to be common and widespread are under-represented in current conservation planning because conservation priority has been biased toward rare and range-restricted species. Increasing evidence suggests that species whose populations are considered stable are declining at rates exceeding those of rare species. Using habitat availability as a proxy for their occurrence, it appears that the three clades are threatened to varying degrees because of habitat loss. Populations from South China and Indonesia are the most threatened due to massive development of lowland habitats. In addition, conversion of wet agriculture to permanent dry crops and the predicted increases in persistent droughts pose threats to amphibian populations in lowland habitats. The extirpated O. lima populations should be restored in Hong Kong by means of reintroduction. A study of the reproductive ecology of O. lima followed by experimental reintroduction is necessary to restore populations and may serve as a model for public education about amphibian conservation. Given the rapid decline of this species in South China, a reintroduction plan and resources to initiate a reintroduction are urgently needed. / published_or_final_version / Biological Sciences / Master / Master of Philosophy

This thesis investigates the potential role of historical isolation of ocean basins in promoting diversification among marine organisms in Southeast Asia. It also questions the possible effects of Pleistocene exposure of the Sunda Shelf on present day marine distributions and genetic diversity. Four species of exploited seahorses (genus Hippocampus), with differing ecological parameters, are used to test historical hypotheses. The results (based on cytochrome b DNA sequencing) suggest that significant phylogeographic structure does exist among seahorse populations in Southeast Asia, but that the patterns are only partially concordant across species. Distinct phylogeographic breaks are seen in H. barbouri, H. kuda, and H. trimaculatus, whereas greater spatial overlap of haplotypes in H. spinosissimus indicates more extensive gene flow. The phylogeographic history of the two shallow water species (H. barbouri and H. kuda) appears to have been primarily shaped by fragmentation and/or long-distance colonisation events. Both species show patterns consistent with hypotheses of divergence mediated by ocean basins separations. The deeper water species (H. spinosissimus and H. trimaculatus) show more evidence of range expansion and isolation by distance. Hippocampus trimaculatus shows a deep east-west phylogeographic division at right angles to that predicted by the separation of the Indian versus Pacific Ocean basins and instead parallels the terrestrial division known as Wallace's Line. Different species have also responded differently to the reflooding of the Sunda Shelf at the end of the last Ice Age: the two deeper water species have colonised it extensively suggesting limited barriers to movement, whereas the shallow water species have not. It is possible that the populations of H. kuda now inhabiting the shelf may stem from populations that found refuge in brackish water lakes when the shelf was exposed to the air. All four species are heav

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