Validation of SNP marker sets for phylogeographic structure and forensic investigations in cheetahs (Acinonyx jubatus).

Ecology and conservation status of cheetah (Acinonyx jubatus)
The cheetah (Acinonyx jubatus) is a member of the Felidae Family and the Order Carnivora (Estes, 1991) and is the last remaining species in the genus Acinonyx (O’Brien, 1983). Five cheetah subspecies have been described primarily according to geographical criteria and morphological differences: A. j. hecki (West Africa), A. j. jubatus (Southern Africa), A. j. raineyi and A. j. soemmeringii (East Africa) and A. j. venaticus (Iran). Phylogeography of cheetah subspecies has been confirmed genetically (Charruau et al., 2011). Cheetah previously had a wide distribution in 44 countries in Africa and Asia and populations numbered around 100,000 individuals in 1900. Historically, the cheetahs distribution has been reported to have been reduced by habitat loss and poaching (Myers, 1975). In the early 1970s, a survey on African cheetahs in sub Saharan Africa revealed that the cheetah had a range of distribution encompassing Western, Eastern and Southern Africa (Myers, 1975). Cheetahs are currently confined to fragmented populations in 29 African countries with remnant populations in Iran and Pakistan (Marker, 2002). By 1998, because of habitat loss and destruction and conflict with farmers, the cheetah population was estimated at 9,000-12,000 individuals (Marker, 1998). Today, the species is listed on Annexure I of CITES and classed as vulnerable (VU) on the IUCN Red List (IUCN, 2010). The Asian population has been reported as almost extinct and it is estimated that only 100 or less individuals inhabit Iran (Marker, 2005). Currently, only limited information is available from North and West Africa concerning the population estimates whereas it is believed that Southern African countries have the highest number of cheetahs in the world, of which Botswana, Namibia, Zimbabwe and South Africa are said to be the major strongholds of cheetah populations (Purchase et al, 2007).

Population genetics in conservation
The first genetic study of cheetah was by O’Brien et al. (1983). The results of this allozyme-based study suggested that cheetah as a species are highly monomorphic, presumably following a historic bottleneck. This low level of diversity was seen as part of the reason for declining numbers (O’Brien et al. 1985; 1986). Later studies using microsatellite markers suggested cheetah are genetically more diverse than previously thought. In this regard, studies by Menotti-Raymond & O’Brien (1993; 1995) revealed considerable genetic heterogeneity for microsatellite markers in cheetah. This variation has been attributed to accumulated variation since the hypothetical bottleneck, resultant from the high mutation rates of microsatellite markers (Hedrick 1996). Merola (1994) confirmed that cheetah genetic variability is very low but in accordance with carnivores’ variability. A central issue in conservation genetics is the amount of genetic variation present, a prerequisite for evolution (Pertoldi et al., 2007; Väli et al., 2008). The rate of adaptive evolution needs to at least match the rate of environmental change in order for a population to persist (Pertoldi et al., 2007). Two potential consequences may be envisioned for loss of genetic variability (i) low genetic variability can be a threat in the long-term for adapting and evolving in disturbed habitats and under changing environmental conditions; (ii) inbreeding may occur in small fragmented and isolated populations, i.e. increased relatedness and homozygosity between individuals as well as autozygosity, posing an immediate threat to such a population (Pertoldi et al., 2007; Väli et al., 2008). An important prerequisite for the design of conservation strategies is information on the speed by which populations become inbred (Pertoldi et al., 2007). A common rescue-strategy adopted by conservation genetics includes the increase of gene flow among populations for the maintenance of genetic diversity and alleviating inbreeding depression (Pertoldi et al., 2007). However, high levels of gene flow can reduce the capacity of populations to stay adapted to local conditions or introduce mal-adapted genes that can reduce viability of populations known as out breeding depression (Pertoldi et al., 2007). A further important issue in conservation genetics is the current structure as well a history of a population or species, both in a demographic and phylogenetic sense (Pertoldi et al., 2007). Evaluation of genetic diversity is therefore common in population genetics and is particularly important in conservation genetics (Väli et al., 2008). Comprehensive management plans for any species of conservation concern should include plans for maintaining existing genetic diversity, both to ensure ability to adapt to changing environments and to preserve the possibility of future speciation (Lacy 1997; Amos and Balmford 2001; Allendorf et al. 2008). Thus, conservation efforts for captive and wild cheetah can be enhanced by accurate and detailed estimates of genetic variability.

Research aims and importance of the expected results
The main scientific goal of the project is to investigate the population structure, genetic diversity and adaptive evolution of cheetah in Southern Africa and validate a subset of 360 single nucleotide polymorphisms for parentage. Knowledge with regards to the genetic variability and connectivity of the different populations is essential in order to make effective conservation management plans for this species. The illegal trafficking of this emblematic species within and outside Africa demands the development of efficient forensic tools for locating parentage and origin of confiscated cheetah samples.
The technical aim of this joint project proposal is to further develop collaboration between researchers and students from Austria and South Africa through personal meetings and team work. The Austria researchers and students will analyse genetic ddRAD sequence data while the South African researchers and students will validate a subset of markers for parentage. We will jointly present our results on international scientific forums including congress presentations and scientific publications. Our joint outreach activities and efforts specifically target a young and female audience, to built awareness for the importance of cheetah conservation and genetics in the next generation. This initiative will prepare the grounds for future collaborations as well as for national and international grant applications.