Name: Lado S

Biodeserts supervisor: Brito JC

Co-supervisor: Melo-Ferreira J, Alves PC

Title: Population history and taxonomy of African hares (genus Lepus) inferred from genetic variation

Institution: University of Porto

Status: Completed



The combination of past climatic and stochastic dispersal events resulted in the contemporary pattern of species diversity and distribution in Africa. The Pleistocene glaciations and the cyclic contractions and expansions of major vegetation zones had deep effects on the distribution and evolution of African mammals. These events dictated the presence of unique biogeographic and climatic areas, making Africa a very special area for biodiversity studies. Despite Africa being generally rich in biodiversity, there is still information deficiency in the organisms that are present, and the diversity and taxonomy of the already described organisms. Additionally, arid regions are normally assumed as plain areas with difficult conditions to sustain life, and therefore with less biodiversity when compared to other climatic regions. However, deserts can be superb endemic species repositories due to the past climatic events, and the Saharan desert is one example. Moreover, the biogeographical intersection between the Palearctic and Afrotropical regions in the Mediterranean basin is considered a hotspot of biodiversity in North Africa. But most of the existing molecular studies on African biodiversity involve vertebrates with low dispersal activity while relevant information on organisms with relative dispersal ability, like hares (genus Lepus), is far from being achieved.

From the 32 Lepus species, 6 are described in Africa. However, the existing studies on this complex genus in Africa were mainly based on evidence of morphology and/or palaeontology, which are limited sources of information, due to the large overlap of characteristics between species. This species classification is far from being well established, and specialists commonly diverge on the number of distinct hares present in Africa, species or subspecies, and their distributions. To clarify the population history of these African hares and consequently contribute to a proper taxonomical classification of these organisms, the identification of the distinct evolutionary entities and their phylogenetic relationships is fundamental. The use of molecular tools therefore appears promising to this end.

Among the African hares, the cape hare (Lepus capensis) is one of the most controversial species. This is one of the most widespread hare species, occurring from Africa to China, with distinct features in different regions that lead to the identification of 80 subspecies. Also, its range distribution is overlapped with other hare species, mostly with L. microtis and L. saxatilis in Africa. However, the level of differentiation and divergence within the cape hare as it is currently classified along its broad distribution is unknown. In order to better understand the evolutionary history of African hares and provide valuable information to clarify its taxonomy and systematics, the population structure and phylogeographic patterns of the species was investigated, inferring the demographic history of the populations in light of the large-scale climatic fluctuations of the Pleistocene. This genetic diversity was in addition analyzed in the context of the putative neighboring species. For this, the broadest sampling scheme ever performed in L. capensis was designed, including both museum and field collected samples and comprising several populations across Africa, with a particular focus on Northwest Africa, and sequences of other 4 Lepus species. The molecular characterization was performed with 18 newly developed microsatellites and sequences of 1 mitochondrial DNA and 5 nuclear DNA loci.

The results revealed strong biogeographic structuring at the genetic level, inferred from the microsatellite data using Bayesian clustering methods, and deep divergences based on both on mitochondrial DNA alone and on the set of sequences from 5 nuclear DNA loci, based on phylogenetic analyses. Five major geographically explicit groups were identified: Near East, Arabia, Kenya, South Africa and Norwest Africa. These inferred high levels of intraspecific divergence suggest that L. capensis is a heterogeneous evolutionary entity that possibly represents several cryptic species. Several divergent lineages which probably diverged in the last million years were found to be geographically structured, which likely resulted from fragmentation of ancestral ranges and divergence in allopatry. Possible barriers to gene flow were also described. Regions where mtDNA haplotypes from different clades were found in sympatry probably result from secondary contact of the divergent lineages after expansion. Whether these evolutionary entities are reproductively isolated and should be considered distinct species should be assessed in the future using a detailed characterization of their genomes, morphology, biology and ecology. This is particularly relevant for the Arabian population, which appears strongly divergent and is also morphologically distinct. Furthermore, mtDNA variation suggested additional genetic fragmentation in the species‘ range in Northwestern Africa, contrary to the homogenous gene pool suggested by the microsatellite analysis. This may result from female philopatry and male-mediated dispersal. Interestingly, some mtDNA lineages were found to be phylogenetically more closely related to other species. The hypothesis of mtDNA introgression, a common event in hare species, into the Near East population was tested using coalescent simulations, and revealed that mtDNA flow occurred from neighboring Lepus europaeus. Thus, taxonomical considerations and the reconstruction of the evolutionary history in this work also involve other neighboring hare species of L. capensis, both African (L. saxatilis, L. microtis) and non-African species (L. timidus, L. europaeus).

The molecular tools applied in this study shed light onto the species boundaries, evolutionary history, phylogeography, taxonomy and systematics of cape hares in Africa as well as of the neighboring hare species. The results contributed to the knowledge on the role of the landscape dynamics of the Sahara desert in the diversification of hares of the region, and how the mountain and water systems together with changes in the climate mediated the diversification. The evidences obtained open the door for more robust and thorough studies aiming at a deeper understanding of North African hare species and that seek to determine whether L. capensis should be decomposed into several taxonomic units.