To the south, the Congo system borders to the Zambezi drainage system, which runs ~2600 kilometres, covers an area of 1.3 million square kilometres, and includes the southernmost of the Great Lakes, Malawi. The Nile system receives water from Lake Albert and Lake Victoria and drains a region of ~3.2 million square kilometres for almost 7000 kilometres northwards to the Mediterranean Sea. It drains part of the EARS (including Lake Tanganyika) and borders to the Nile system in the northeast. The Congo River covers an area of ~3.7 million square kilometres and has a length of ~4100 kilometres. The three largest drainage systems in present-day Central Africa are the Congo-, the Nile-, and the Zambezi system (Figure 1). Rifting created, disrupted, redirected, and connected major freshwater systems. The climatic, geological, and hydrological consequences of the rifting processes are critical to understand the emergence of the endemic species of the savannahs and the Great Lakes as well as the origin of humankind. The formation of the East African Rift System (EARS) played a decisive role in the evolution of Africa’s tropical fauna and flora. Amongst others we argue that the closest relatives of present day viviparids in Lake Malawi are living in the Middle Congo River, thus shedding new light on the origin of the endemic fauna of this rift lake. Finally, we review similarities and differences in patterns of vertebrate and invertebrate dispersal. By integrating our results with previous findings on palaeohydrographical connections, we provide a spatially and temporarily explicit model of historical freshwater biogeography in tropical Africa. The current study testifies to repeated disruptions of the distribution of the Viviparidae during the formation of the East African Rift System, and to a central role of the Congo River system for the distribution of the continent’s freshwater fauna during the late Cenozoic. Our phylogeny covers localities from major drainage basins of tropical Africa and reveals highly disjunct sister-group relationships between (a) the endemic viviparids of Lake Malawi and populations from the Middle Congo as well as between (b) the Victoria region and the Okavango/Upper Zambezi area. This group allows reconstructing drainage patterns exceptionally well because it disperses very poorly in the absence of existing freshwater connections. We study these biogeographical patterns using a fossil-calibrated multi-locus phylogeny of the gastropod family Viviparidae. However, it remains unclear how rifting affected the biogeographical patterns of freshwater biota through time on a continental scale, which is further complicated by the scarcity of molecular data from the largest African river system, the Congo. The formation of the East African Rift System has decisively influenced the distribution and evolution of tropical Africa’s biota by altering climate conditions, by creating basins for large long-lived lakes, and by affecting the catchment and drainage directions of river systems.
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