The large amount of environmental change that has occurred during the Pleistocene, in which tropical forests and grasslands have repeatedly contracted and expanded, has dramatically shaped the biodiversity of tropical ecosystems. Notably, biodiversity is geographically structured as a consequence of divergence in allopatric refugial habitats. There are frequently cryptic taxa, i.e. taxa that are morphologically indistinguishable but can be revealed by methods such as DNA barcoding and population genetics to have been evolving separately for long periods of time. There are also often morphologically distinct forms for which the importance of separate conservation status is unclear, for example multiple pelage patterns in Callosciurus finlaysonii squirrels in Southeast Asia or different subspecies of giraffe within the four recognised giraffe species in Africa. This PhD would select a high biodiversity ecosystem to study to determine the historical factors shaping genetic diversity within and among closely related species and how this information can be applied to long term conservation goals. Particular systems of interest are tropical forest biodiversity in Southeast Asia and savannah biodiversity in East and Southern Africa. In Southeast Asia the past fragmentation of forests has greatly influenced the pattern of forest biodiversity resulting in clines of genetic diversity, zones of secondary contact and highly genetically distinct allopatric populations/taxa (e.g. Morgan et al. 2011).In Africa, environmental change has also led to periods of allopatric divergence and genetic admixture for both forest and grassland species (e.g. Bennett et al 2016; 2018). In Africa the Rift Valley system has also likely acted as a barrier to gene flow and contributed to genetic differentiation. Taxa could include (but are not limited to) flying squirrels in Southeast Asia and birds (e.g. lilac breasted roller) or giraffe in East Africa. The project would involve: sampling from natural populations and/or the use of museum specimens; generation of genetic data using mt DNA, microsatellite or genomic sequencing; and population genetic, landscape genetic and phylogenetic analyses. The information and understanding gained would be applied to identify optimal conservation strategies that maintain the distinctiveness of cryptic and non-cryptic biodiversity and ensure continuation of the evolutionary processes, particularly involving local adaptation, that are already underway
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