In Partial Fulfillment of the Requirements for the Degree of Doctor of Philosophy in Biology (Applied Genetics)

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Addis Ababa University


Three Lepus species are currently considered to occur in Ethiopia: Lepus habessinicus Hemprich and Ehrenberg 1832 (Abyssinian Hare), L. fagani Thomas 1903 (Ethiopian Hare) and L. starcki Petter 1963 (Ethiopian Highland Hare) based on limited morphologic and cytogenetic data. Analyses of morphological characters, 13 microsatellite loci, one mitochondrial (ATPase sub-unit 6 sequence) and five nuclear sequences (Transferrin (TF), Thyroglobulin (TG), Uncoupling protein two (UCP2), Uncoupling protein four (UCP4) and Thyroid stimulating hormone beta (TSHB)) were made to provide an initial comprehensive data on the evolutionary relationship among the three hare species collected from twenty six localities in Ethiopia and identified by their external phenotypes, dental and skull characters. In addition, other Lepus species: L. capensis, L. saxatilis, L. europaeus, L. timidus and L. victoriae were used for phylogenetic comparison. Multivariate skull morphometric analyses (PCA & DA) of seven Lepus species (n = 327) indicated clear distinction among the species. Lepus habessinicus had a distinct morpho shape space relative to L. capensis. Lepus fagani had a distinct morpho shape space relative to L. saxatilis and L. victoriae. Lepus starcki had a distinct morpho shape space relative to L. europaeus and L. capensis. Microsatellite analysis based on hares (n = 107) collected from Ethiopia resulted in clusters of hare species in accordance with population origin and collection sites. Individuals of L. habessinicus and L. fagani were substructured in accordance with population of origin and collection localities with some degree of SSR introgression among each other. Microsatellite introgressions were documented also between species. In all analyses (structure, FCA and NJ) L. starcki individuals were consistently clustered into a single group. All phylogenetic reconstruction methods used (Neighbour Joining, Maximum Likelihood, Bayesian Analysis and Median Joining Networks) by and large resulted in similar topologies for mitochondrial and nuclear sequences, respectively. The three hare species from Ethiopia were not monophyletic for both mitochondrial and nuclear sequences, but showed signs of both unidirectional and bidirectional introgressions among each other. Lepus habessinicus carried mtDNA distinct from South and North African L. capensis, with no sign of introgression, contrary to earlier suggestions to include L. habessinicus under L. capensis. Similarly, L. starcki had distinct mtDNA relative to L. capensis and L. europaeus as opposed to previous suggestions to include L. starcki either under L. capensis or L. europaeus. Despite the morphological distinctness of L. fagani, it shared a substantial proportion of mtDNA and nucDNA with hare species from Ethiopia and L. saxatilis from South Africa. The nuclear sequences revealed phylogenetically and geographically meaningful clusters, albeit with a fair amount of indications of recent or historical introgresions among the species. In line with ATP, the nuclear sequences indicated close phylogenetic relationships among the three Lepus species from Ethiopia, with L. fagani being surprisingly tightly connected to L. habessinicus. Furthermore, the microsatellite analysis indicated low levels of genetic differentiation (G’ST and Dest 0.384 and 0.334, respectively) between L. habessinicus and L. fagani. Moreover, the nuclear sequences suggested a closer evolutionary relationship of Cape hare from north and south Africa to hare species in Ethiopia. Although the nuclear sequence analyses supported the North American ancestry of Lepus, the results of the present analysis also suggested Africa as a potential ancestral area of Lepus. Overall, both multivariate skull morphometric and molecular analyses suggested a specific status of L. habessinicus, L. fagani and L. starcki. Keywords: Ethiopia, introgression, Lepus habessinicus, Lepus fagani, Lepus starcki, microsatellite, mtDNA, nucDNA, phylogenetics, phylogroup and skull morphometry.