The population genetic structure of living organisms is largely shaped by both historical and contemporary gene flow in the species range . Furthermore, the factors structuring the genetic diversity are also able to play a key role in the process of diversification, adaptation and speciation . Identifying the interactions between those factors is crucial to understand the evolutionary history of a species . On the one hand, the extrinsic factors, such as climatic and geological events, shape the large-scale population differentiation pattern [4–6]. On the other hand, both extrinsic (e.g. habitat heterogeneity), and intrinsic factors (e.g. dispersal capability, mating system and habitat preference) have an impact on gene pool composition at intra-population level or over short time periods [4, 7–9]. Species with wide distribution and high dispersal capability are supposed to exhibit genetic differentiation at the paleo-biogeographic scales, with limited micro-geographic structure. On the contrary, species with limited distribution and restricted dispersal capability and/or specific mating behaviour are supposed to exhibit strong genetic structure both at micro-geographic and temporal scales. However, species with a wide distribution area and specific life history traits (e.g. restricted dispersal, limited population size) are expected to exhibit more complex genetic diversity pattern.
Cichlid fishes are well known examples of complex population genetic structure among African ichthyofauna. Lake-wide studies have revealed the impact of paleo-historical lake level fluctuations on genetic diversity (e.g. ). Small scale investigations have revealed the importance of both habitat heterogeneity, ecology and dispersal capability on population differentiation (e.g. ). To date, however, very few studies have investigated the factors responsible for the population genetic structures both at the micro- and the macro-geographic scales at the same time. They often represent only a relatively restricted paleo-biogeographic scale .
The Nile tilapia, Oreochromis niloticus (Linnaeus, 1758), is an interesting model-species to study the interactions between intrinsic and extrinsic factors on the structure of the natural populations from a local and temporal to a broader biogeographic scale. This economically important fish has one of the largest natural distributions among African fresh-water fishes, covering the entire Nilo-Sudanian province (from Senegal to Nile basins), the Ethiopian Rift Valley province, the Kivu province, north Tanganyika province (Ruzizi) and the Northern part of the East African Rift Valley. This species shows an exceptional capacity of adaptation, which allowed its colonisation of a wide range of habitats from small forest rivers to large drainage and lakes, as well as alkaline pools with hot springs [13, 14]. The description of seven sub-species based on eco-morphology  largely reflects their adaptive divergences.
Due to its great interest for aquaculture and fisheries, the Nile tilapia and a few other tilapia species have been introduced outside their natural distributions . Introduced tilapias have become invasive especially in areas originally not containing any tilapiine cichlid, within as well as outside Africa. In area inhabited by congeneric tilapias, on the other hand, they have often led to hybridisation with the local allopatric species . However, between sympatric congeneric species of tilapias, signature of hybridisation has only been reported at evolutionary time scale, not at current ecological time scale. This is especially the case of the ancient mitochondrial introgression from O. aureus into O. niloticus populations restricted to West Africa, whereas the 2 species are also sympatric in the Nile River. This introgression has certainly happened during the drastic water level fluctuations of the Pleistocene . But neither recent natural hybridisation event nor successful translocation of any allopatric tilapia (i.e. Oreochromis spp.) within the natural distribution of O. niloticus has been reported so far .
As most of the cichlid fish, the Nile tilapia exhibits interesting and complex life history traits, and especially well-developed social behaviour [13, 14, 17–19]. During reproduction, males show strong territoriality and females provide elaborated parental care (i.e. maternal mouth-brooding and guarding) . Because of this reproduction behaviour and substrate affinity, the Nile tilapia is considered a rather sedentary species . In addition, the lekking behaviour of males to attract females for reproduction suggests the existence of a certain level of sexual selection [17, 20]. These life history traits are expected to strongly affect the population dynamics of this species, via limited dispersal or reduced effective population size.
From the paleo-geographic point of view, Africa has experienced severe hydrogeographic modifications since the Pleistocene. The East African Rift valley has been subject to many tectonic disruptions of the water basins with inversion of the course of some rivers in the Nile basin (sensu lato), whereas the Sudano-Sahelian region experienced dramatic climatic fluctuations with alternating humid and dry phases [21, 22]. By their drastic modifications of the extension and connectivity of the different water-basins, all these paleo-geographic and climatic events have undoubtedly affected (1) the distribution of fish species in these ichthyofaunal provinces [23, 24] and (2) their population genetic structure.
Previous studies have suggested an influence of paleo-geographic events on the historical distribution of Nile tilapia, based either on morphological traits  or on moderately polymorphic molecular markers, i.e. allozymes and mtDNA, [16, 25–28]. At the opposite, micro-geographic population structure has been reported in lacustrine populations of another tilapiine species, Sarotherodon melanotheron, with similar life history strategy, implying non-random mating . However, to date, the relative importance of these paleo-geographic events and the factors influencing the micro-geographic structure of the current populations is not well understood.
In this study, we investigated the spatio-temporal genetic structure of ten natural populations of O. niloticus, which cover the main part of the species' natural distribution in Africa. By investigating both spatial and temporal genetic diversity based on nine microsatellite loci, we aimed (1) to understand the current population genetic structure of O. niloticus in its natural habitat range in Africa and (2) to evaluate to what extend the population genetic structure was shaped by the paleo-geographic events and the current geographic connectivity at the different spatio-temporal scales. We also discuss potential roles of life history of the species in the species-range population genetic differentiation.