1 Appendix: Supporting Information Drake Et Al SI Text 1

Home , Chalcides ocellatus, Echis, Raiamas senegalensis

Appendix: Supporting Information

Drake et al

SI Text 1) Trans-Saharan Species Distributions Maps of the fauna of North Africa have been compiled from Van Damme (1) and Le Berre (2) with additional distributional and species information from more up to date sources (3 to 9). This information was evaluated to identify species found north and south of the Sahara, along the Nile, in isolated oases within the desert, and combinations of the above spatial distributions. A comprehensive literature review of these species was then conducted to assess the numerous changes in their status since publication of their ranges. Some species had been subdivided, thus their names and ranges needed to be updated. Sometimes they no longer had a spatial distribution indicative of trans-Saharan migration and these species were discarded. For example Lemniscomys barbarus was originally thought to be found in the Maghreb and the Sahel but was subsequently found to consist of two species, Lemniscomys zebra south of the Sahara and Lemniscomys barbarus to the north (10).

Other phylogenetic studies revealed contrasting results indicating that animal populations to the north and south of the Sahara were closely related; thus suggesting their recent dispersal across the desert. For example, the morphological variation in the leaf-nosed bat, Hipposideros caffer and H. rubber, has led to suggestions that this species complex may contain more than two species. Phylogenetic analysis suggests four distinct lineages (11). Two distinct sister clades are found within H. caffer with Hipposideros caffer caffer restricted to southern Africa and Hipposideros caffer tephrus inhabiting the Maghreb, the Sahel and Arabia and thus retaining a trans-Saharan spatial distribution for one leaf-nosed bat species.

In some cases comprehensive genetic studies have been conducted on trans-Saharan animal species that requires their wholesale reassessment. It was initially thought Chalcides ocellatus was found both north and south of the Sahara and in refuges within the desert (2). However, phylogenetic analyses found it to be a clade, exhibiting as much depth as the three other main clades of Chalcides, and having at least six main lineages (6). The species is thought to have originated in Morocco where it diverged into a xeric (C. o. ocellatus) and mesic (C. o. tiligugu) unit at about 2.3

1 Ma. An independent lineage spread eastwards into the Tunisian region at about 4.6 Ma and then along the Mediterranean coastal region to Egypt by around 3Ma, where it divided into two subclades at around 1.4 Ma. One of these migrated to Israel, and the other to Turkey and Cyprus. There is little genetic information on the Sub-Saharan species of C. ocellatus, and it is thus not possible to say when they migrated across the Sahara. However, one Saharan clade does suggest recent trans-Saharan dispersal. It consists of southern Egyptian and southern Mauritanian samples of. C. ocellatus humilis, which separated from other species in the C. ocellatus group at about 4.6 Ma. Even though the two samples are 4200 km apart on opposite sides of the Sahara, they are genetically similar, suggesting either a relatively recent spread, or that they were in contact until recently. C. o. humilis now has a fragmented range which may be attributable to its spread across the Sahara in a recent humid period and subsequent isolation by aridification (6).

The results of this literature review are presented in Table S1 that lists fauna showing a trans- Saharan species distribution and infers the most likely dispersal route from this distribution.

2) Aquatic Animal Dispersal Mechanisms Although exchange of fish between the Nile, Chad, Niger, Volta and Senegal basins and the waterholes of the Sahara during the Quaternary has long been accepted in order to explain the similarity in their ichthyofauna (12), the method by which this was achieved has not been satisfactorily explained until now. Theoretically it can be explained by fish dispersal overland, through tornadoes transporting water and associated wildlife (13) or by specialist adaptations (14). Clarid fish can employ terrestrial locomotion, while cyprinodonts have drought-resistant eggs that can be transported in mud attached to birds’ feet and fish can be dropped alive by birds, a particularly effective method of dispersal for mouth brooding cichlids whereby a large number of individuals can be transported at one time (14). However, these potential modes of transport do not appear to be at all effective globally because the vast majority of neighbouring basins have significantly different ichthyofauna, as is the case in nearby basins in West Africa (15). Because cyprinodonts can be dispersed by birds they should be the least likely fish to exhibit such spatially restricted species distributions, yet most cyprinodonts have limited distributions (14). Thus, although it is feasible for fish to be dispersed by birds, in practice it is rare. The more likely and most practiced means of dispersal is for fish to migrate from one region to another by water connections. The biogeography of fish can thus provide valuable information on palaeo-drainage patterns (12). Therefore the presence of Tilapia zillii, Clarias gariepinus, Hemichromis

2 letourneauxi and Raiamas senegalensis throughout much of the Sahara (Table S1)) suggests widespread hydrological connections.

Freshwater molluscs are more diverse in their modes of dispersal (1). Like fish, some molluscs require permanent hydrological connections whereas others can use temporary water interconnections. Many freshwater molluscs require no connections at all, being transported by attachment to birds, amphibians, water insects and perhaps large aquatic animals such as hippopotamus and crocodile (1). Some mollusc species have evolved to be transported by animals; freshwater pulmonates lay desiccation-resistant sticky eggs that adhere to birds and are thus carried by them, whilst hard-shelled snail species can pass through fish digestive systems undamaged and Sphaeriids can to attach themselves to the gills and fins of fish (1).

Van Damme (1) concludes that these different dispersal mechanisms can in some cases provide indications of different palaeo-hydrological conditions. Most common Saharan extant and fossil molluscs, such as all Pulmomates and Melanoides tuberculata (Fig. S5)), are readily dispersed overland and do not constitute strong evidence for the presence of major permanent river systems. Thus it is no surprise that these species are found throughout the Sahara and much of the more humid regions that surround it. Given the different dispersal mechanism from fish the similarity in Saharan fish and mollusc biogeographical provinces is surprising (main text Fig. 3 and Fig. S5) and could indicate that the animals that dispersed these molluscs followed the interconnected trans- Saharan river system believed to have been used by the fish. The presence of Bellamya unicolor, Cleopatra bulimoides, Pila and Lanistes, however, are indicative of stable, long-term hydrological links. They are restricted to the southern Sahara (Fig. S13) suggesting that it was only in this part of the Sahara were the links were deep and durable.

3) Palaeo-hydrological Mapping The recent availability of free digital topographic data and satellite imagery for the entire Sahara has allows an integrated assessment of its palaeo-hydrology for the first time. To achieve this we have interpreted 3 arc-second Shuttle Radar Topography Mission (SRTM3) digital elevation model (DEM) (16,17) and Landsat Thematic Mapper (TM) satellite imagery. The SRTM3 DEM was used to identify palaeo-river channels, closed basins that would have been likely places for lacustrine sedimentation, palaeo-lake shorelines and spillways. Interpretation of Landsat TM false colour composite (FCC) imagery provided further information on palaeo-river systems. Remote sensing was particularly useful for mapping lake sediment outcrops, as the resulting limestones and

3 gypsum-rich sediments are readily discriminated from other materials in Landsat FCC imagery. Where the palaeo-hydrology has already been studied we have integrated our interpretations with the wider literature. Our interpretation of the palaeo-river and lake systems in Libya, the western desert of Egypt, the River Nile catchment and parts of the Chad Basin were guided by references 18 to 28, in southern Mali and Mauritania by 29 to 33; in northern Mali and southern Algeria by 34 to 35 and in northern Algeria and southern Tunisia by 36.

Palaeolake areas were generally estimated from the shorelines evident in the DEM using a thresholding method (37), but when they were not evident other information was employed. For instance the size of the lake in the basin of the Chotts was estimated from the DEM using the reported altitude of the outflow channel (38), while the minimum size of the Ahnet-Mouydir Megalake in Algeria was estimated from the DEM using the altitude of 230m reported for dated lake sediments (39). The latter is a conservative estimate as lake shorelines can be considerably higher in elevation than some lake sediments due to lake bed bathymetry.

To construct the palaeo-hydrological map of the ‘green Sahara’ during the last interglacial the dates (18,38,40) were combined with new data reported in this paper (Fig. S6). Information on locations and descriptions of the sample types and sites was then combined with the palaeo-hydrological map to determine the area of influence the sample represented.

4) Mechanisms for Saharan Palaeo-hydrological Links A number of different mechanisms for the transfer of water-dependant biota between basins have been proposed, most commonly lake overspill, river capture and tectonics (3). It has not generally been recognised that large alluvial fans, which are prevalent in the Sahara, also provide a very effective mechanism. The Sahara desert, and the river basins that feed water into it, contain 17 such palaeo-fans (main text Fig. 1), all of which were very large with seven being larger than the present day Okavango Delta, the largest active sub-aerial fan in the world (56).

When a river channel encounters the apex of an alluvial fan it becomes less confined and its gradient decreases. Both these changes affect channel form and dynamics in ways that promote the probability of linkages between otherwise separate river systems. The lack of confinement allows the main channel to split into numerous distributary channels that spread out over the fan surface. If a fan lies on the boundary between two river catchments, its distributary channels can link adjacent river systems, thus allowing aquatic organisms to transfer from one basin to the next. The

4 contemporary Okavango Fan provides an example of this; having a distributary channel called the Selinda Spillway that links the Okavango River to the Zambezi River (via its tributary the Kwando River) when the Okavango experiences high discharge. Inspection of the Landsat MSS and TM archive shows that since the first sensor was launched in 1972 these two river systems have been linked at least three times (in 1976, 1979 and 2008). The Okavango-Zambesi hydrological links currently do not last very long because of the episodic nature of the discharge, however, during more humid periods they would be more permanent and thus more effective.

Fan channel systems are highly mobile and provide a further mechanism whereby biota are transferred between basins. Channel migration can lead to a change in the basin fed by a fan, allowing aquatic organisms contained in the channel reaches above the fan to move downstream into the new basin. The nature and rate of channel dynamism is controlled by fan geomorphology and is characterised by both gradual migration and more sudden switching. Three categories of fan have been recognised (56); debris flow dominated, braided river dominated and meandering river dominated fans. Debris flow dominated fans are small and steep and as such are not like Saharan palaeo-fans. The giant palaeo-fans of the Sahara have the very low gradients that are typical of meandering fans, however, they exhibit palaeo-channel forms that can be either braided or meandering or a combination of both and thus exhibit some characteristics of braided fans.

The channels on meandering and braided fan systems are highly mobile but the processes that drive this mobility differ. On meandering river fans the distributary channel switching is a result of channel aggradation (57). This occurs because channels rapidly become confined by vegetation and associated peat deposits that restricts deposition of sediments to the channel bed and causes it to aggrade. Aggradation results in a reduced channel gradient, a lower flow velocity and invasion of aquatic plants. These processes ultimately cause the channel to become choked and fail, with a secondary channel developing where a breach occurs (57). Within the Okavango Fan, where this mechanism was first observed, present channel lifetime is about a hundred years (57). Braided fan systems are generally steeper than meandering river fans and are dominated by fluvial processes with vegetation playing only a minor role (56). Like the other fan types, the channels in a braided fan system are highly mobile. For example, on the Kosi Fan in northern India the Kosi River shifted 110 km between 1736 and 1964, and in 2008 the channel switched back into an old palaeo-channel causing serious flooding.

5 One of the most important palaeo-fans in the Sahara is the Southern Darfur Fan (Fig. S1) as it can link the Nile and Chad Basins. Its surface is covered in relict meandering rivers and thus would have experienced processes typical of a meandering fan when flow was permanent, presumably during the ‘African Humid Period’ between 10 and 4 ka when the African Monsoon penetrated much further north than it does today (58). The fans meandering distributary channels appear to feed into both the Nile and Chad Basins (Fig. S1) and thus could have linked these river systems during humid periods in much the same way as the Okavango Fan links river systems today.

The Darfur Fan is located in the Sahel, just to the south of the Sahara and experiences periodic rainfall and ephemeral flooding today. A Landsat TM image from 1986 has captured it in flood, revealing two prominent active channels (Fig. S2), and suggesting that channel switching at the fan apex could also have transferred biota between the Chad and Nile Basins. An ephemeral channel drains the south-western margins of Djebel Maara skirting the western side of the fan and feeding into the Chari River (Fig. S2) which goes on to discharge into Lake Chad. Another ephemeral channel drains the south-eastern flank of the volcano and floods the western side of the fan (Fig. S2) before flowing into the Nile via the Sudd Swamps. At their closest point these two channels are only seven kilometres apart and thus it does not require much channel migration to switch river systems. Furthermore, the region between these two channels is covered in well-developed palaeo- channels that appear to have linked them in the past (Fig. S2), suggesting that channel switching between basins has occurred on a regular basis.

At the fan apex the two river channels occupy the same flood-plane with no significant topographic barriers between them. Thus during periods of exceptional flooding when the entire flood-plane is inundated the channels would be linked by a continuous body of water that would allow transfer of water-dependant organisms between otherwise separate river systems. Thus at times during the Holocene either divergent distributary channels, channel switching or flooding at the fan apex could have allowed transfer of aquatic biota between the Chad and Nile basins, thereby explaining the similarity of the aquatic fauna of the two basins. Of the 115 fish species identified in the River Nile, 86 are also found in the Chari River (14) while the malacofauna of the Sudd is an impoverished version of the fauna of Lake Chad and shows only a superficial similarity to that found in other parts of the Nile (59).

Other mechanisms have been suggested that could explain this similarity in fish fauna, such as the capture of Nile tributaries by the Chari River upon the uplift of Djebel Maara in the Miocene (60)

6 and a mid-Tertiary trans-African drainage system that would have had its headwaters in the Red Sea Hills and a southwest orientated main channel flowing into the Chad Basin and thence on into the Atlantic via the Niger Delta (61). However, these connections happened so long ago that they do not readily explain the lack of endemism in each basin. They also fail to explain the similarity of the malacofauna between the Lake Chad and the Sudd region of the Nile, but not other parts of the Nile system. Recent connections via the Darfur Fan explain both these points, providing a mechanism that could have periodically linked Nile and Chari River since the development of Djebel Maara during the Miocene.

The Niger River Inland Delta is a fan that shows evidence that it once linked the River Niger to the Senegal River. The Niger River becomes unconfined at the fan apex where it bifurcates into many braided palaeo-channels, only one of which is currently active (Fig. S3B). This active channel crosses the fan before terminating in a birds foot delta on the margins of Lake Debo at the fan base (Fig. S3B). When the other palaeo-channels were active, the Niger would have flowed further to the north into the Mema region (also known as the ‘dead delta’). The largest of these palaeo- channels is known as the Fala de Molodo and is thought by some to have carried the main flow of the River Niger into the Hodh Basin and then into the Azaoud basin where it once fed a giant lake in the Taoudenne Depression during the late Pleistocene (29,30,32). This theory explains many aspects of the channel networks evident in the satellite imagery and DEM but defies the topography (Fig. S3A). The combined channel and topographic data suggests a slightly different scenario whereby the Fala de Molodo once flowed into the Hodh and thence into the Senegal River thus linking these two rivers and explaining their similarity in fish fauna (14). This scenario is similar to that postulated by Macdonald and Allsworth-Jones (62) who suggested links between the River Niger and the Senegal both directly and via the Fala de Molodo. The DEM shows evidence for the latter connection but not the former. The main Fala de Molodo palaeo-channel skirts the edge of the Mema along the base of a ridge that separates the Mema from the Erg of Azaoud to the north (Fig. S3A and B)). At various points the channel splits only to merge again further down its course. At one of these bifurcation points the northernmost channel feeds a palaeo-lake that sits within a pass in the ridge (Fig. S3B). The water in the lake is prevented from flowing further north through the pass by a field of sand dunes. If the dunes were not there the channel would have flowed through this gap and into the Senegal River; the headwaters of its tributaries being are a mere 12 km away on the other side of the dunes. Given the similarity in fish fauna between the Niger and Senegal Rivers it is likely that this happened recently, before the dunes blocked the pass.

7 It is evident from this interpretation of the DEM (Fig. S3B) that the redistribution of sand during arid periods can affect the reestablishment of rivers during subsequent humid periods by blocking and/or diverting their previous course (33). Indeed Lake Debo was formed by dunes that were built during the last glacial maximum and subsequently blocked the Niger River when it started to flow again at the end of the glacial period (33). This led the formation of Lake Debo behind this dune barrier during the Late Pleistocene and early Holocene. Initially the lake was probably very large (30) (Fig. S3A), however, down cutting of the overspill channels and the aggradation of the Niger River Fan into the lake have both led to a significant reduction in its size (Fig. S3B).

The sand dunes that block the postulated link between the Rivers Niger and Senegal are part of the same dunefield system as those that blocked the Niger River to form Lake Debo and therefore are presumably the same age. Thus it is reasonable to assume that the Niger River would have been connected to the Senegal River through this pass prior to the last glacial maximum and that subsequently the dunes blocked both the pass and the River Niger valley to form Lake Debo and the lake in the pass. The shoreline of the latter lake is at an altitude of 274m whilst the lowest point on the dunes that separates the lake from the Senegal River headwaters is 283m, a mere 9 meters higher. The low point on the dunes that blocked the River Niger and formed Lake Debo is 266m, only 8 meters lower than the dunes in the pass. Thus if the lowest point in the dunes that dammed the pass had been a mere 8m lower they would have formed a less formidable barrier than the dunes that formed Lake Debo and the Niger River would have overspilled into Senegal River during the early Holocene rather than taking its current course. This further illustrates that the formation of sand dunes during arid periods can affect the course taken by rivers during subsequent humid periods, sometimes causing them to divert into another basin. As long as the headwaters of these rivers always lie outside the desert (as both the Niger and Senegal Rivers do), this process can transfer aquatic biota that survive in the headwaters from one basin to the next during subsequent humid episodes.

The largest of all the Saharan palaeo-fans is the Tanezrouft Fan that drains the western side of the Ahaggar Mountains (Fig. S3A). Indeed the palaeo-fan is probably the biggest sub-aerial fan on earth with an area of 189,300 km (2), compared to 22,000 km2 for the Okavango Fan (56). The fluvial system on this fan surface is highly complex and was first recognised using satellite imagery (34). The system can now be studied in more detail using the SRTM DEM that allows two crucial bifurcation points to be recognised (Fig. S3A). The first is where runoff from the Ahaggar Mountains is diverted both to the south-west towards the Erg of Azaoud in Mali and north-

8 westwards further down-fan to the second bifurcation point. At the second bifurcation point runoff is directed both down fan into Ahnet-Mouyder Basin and along the Djouf bis River and into palaeolake Fersiga North (Fig. S3A). Thus the fans drainage network could at times have linked the paleao-rivers and lakes in the Erg of Azaoud to the Ahnet-Mouyder Basin that is in turn linked to the Atlas Mountains by the Saoura River. The Erg of Azaoud fluvio-lacustrine network appears to flow into the River Niger (Fig. S3A) thus potentially providing intermittent hydrological links across the Sahara. The Erg contains a complex interconnected network of rivers, swamps and lakes fed by the Tazenrouft Fan rivers as well as those draining the Adrar des Iforhas Mountains and ultimately discharging into the Niger Delta (Fig. S3A). Away from the mountains much of the sand sea is very flat promoting sluggish rivers, the development of swamps and probably backflow down the channels near the Niger Delta into the Erg of Azaoud when the River Niger was in flood. The Erg of Azaoud river system must have been deep as Holocene fossil evidence shows that it allowed deep water fish such as Nile Perch to penetrate from the Niger through to the northern margins of the sand sea (14) (Fig. S12) and to access the rivers that drain the Ahaggar Mountains, presumably via the Tanezrouft Fan. However, such deep-water animals do not appear to have used the northernmost bifurcation point to access the Ahnet-Mouyder Basin suggesting that it was less permanent or that the water connections were shallow.

There are many fans in the Sahara similar to those described above, some of which could have linked adjacent river systems (main text Fig. 1). Though all these landforms have been mapped as fans some lack the fan shape (e.g. the Serir Tebesti, main text, Fig. 1) and in parts are more like braid-plains, however, they all exhibit bifurcating channel networks that when active would have been highly dynamic, this being their most important characteristics for facilitating dispersal of water dependant organisms.

Lake overspill provides another method for linking adjacent catchments (3). It is important in creating the interconnections in the Erg of Azaoud fluvio-lacustrine network (Fig. S3A and B). In terms of inter-connecting large areas the most effective overspill comes from Lake Megachad. Dates from high-stand shorelines (63, 64, 65) indicate Lake Megachad spilt over into the Benue River during much of the early and middle Holocene, linking the Chad Basin (2,480,300km²) to Niger River Basin (2,561,200km²) and creating the second largest river system in the world (5,041,500 km²; main text Fig. 1; the Amazon being the largest at ~ 6 million km²). With the Chad basin also intermittently linked to the Nile River via the Darfur Fan, it is possible that if both these connections were active at the same time they would have created the world’s biggest

9 interconnected waterway at ~9 million km² (main text Fig. 1). Another large-scale example is Lake Megafezzan, a giant lake that existed in the Fezzan Basin in Libya during the middle Pleistocene (19). If this lake were ever large enough to overspill it would have done so into the Serir Tibesti River that was also periodically linked to the Kufra River by a giant fan (main text Fig. 1), thereby connecting the fluvial systems of the vast majority of Libya (19).

The final process that provides important links between some Saharan basins is neo-tectonics. When faults and rivers both occur on the divide between basins, surface movements can lead to the river diverting from one basin to another. This situation appears to connect the Ahnet-Mouydir Basin with the Basin of the Chotts and the latter basin to the Fezzan Basin. The Ahnet-Mouydir and Chotts link occurs along the course of the River Igharghar, the main river draining the northern slopes of the Ahaggar Mountains which terminates on the margins of Chott el Djerid (Fig. S4). On the northern margins of the mountains the river runs along a fault scarp that forms the catchment divide between the Ahnet-Mouydir and Chotts basins. At one point the fault truncates a valley that feeds into the Ahnet-Mouydir Basin. The headwaters of this valley are only three meters higher than the channel and a mere 80 meters away from it (Fig. S4), thus a minor change in the topography caused by fault movement would allow the headwaters of the River Igharghar to flow into the Ahnet-Mouydir Basin. The presence of a large relict fan at the downstream end of this valley suggest that the river did indeed once flow in this direction.

A similar tectonic situation links the Basin of the Chott to the Fezzan Basin. In this case the Wadi Tanezzuft is susceptible to diversion along a small part of its course that runs beside a fault that marks the boundary between the Chotts and Fezzan Basins. Currently, the wadi drains parts of the Accacus and Tasili n’Ajjer Mountains before flowing towards the River Igharghar. However small movements along this fault could easily divert the wadi into the Fezzan Basin. Indeed, we have observed extensive rounded gravel deposits at the base of some of the fault scarps on the margins of the Fezzan Basin that suggests Wadi Tanezzuft did indeed once flow into the Fezzan Basin.

In summary four processes appear to facilitate links between Saharan river basins; in order of importance these are flooding and channel dynamics on alluvial fans, lake overspill, channel blockage by sand dunes and tectonics. There are 9 key points in the Sahara where these links occur (main text Fig. 1). Substantial parts of the catchments of these interlinked rivers are found outside the Sahara and these refugia are in an ideal position to re-supply the desert with aquatic organisms when the Sahara turns green. The similarity in aquatic organisms between these river systems and

10 the relict populations found in the Sahara today suggests that this happened recently, most likely during the African humid period when the Sahara was last green. Recent comparisons of fossil fish from the Nile and the Sahara show that similar fish genera and families are found throughout much of this region during the Miocene, Pliocene and Holocene (66), suggesting that these interconnections have been periodically active for a long time.

5) Mapping Holocene Green Sahara Species Distributions In order to determine if water dependant species that are now found north or south of the Sahara, and in Saharan oases, once had a wider distribution across the green Sahara that can be explained by its palaeo-hydrology, their species distributions are overlain on the Late Pleistocene/Early Holocene palaeo-hydrology of the Sahara and compared (Fig. S5-7). To evaluate Holocene faunal distributions this information was augmented with the location of historical sightings, rock art and fossil sites for selected fauna. A wide array of species was investigated including fish, molluscs and savannah mammals. Fauna were chosen according to the number of refuges, sightings, fossils and rock art sites. Only those species that provide enough data to convincingly depict the their current and Holocene range were selected. Notwithstanding this the number of locations where this information is found varies between species. Fifteen species were finally selected (Fig. S5-13).

6) Saharan Archaeology and Linguistics The Aqualithic model (67) recognised the importance of barbed bone points to the Nilo-Saharan people of the south central Sahara. The model also included pottery in the cultural package, as certain styles of pottery (e.g. dotted wavy line) at the time appeared to have a similar spatial distribution to barbed bone points and Nilo-Saharan languages 67. However, it has since become clear that pottery is an innovation that spread extremely rapidly in a zone between northern Mali, the Air Mountains and the Nile at least 11,500 years ago (68,69), initially attaining a spatial distribution which intersected that of barbed bone points (e.g. dotted wavy line pottery in Fig. S14). Although an important technical innovation, other styles of pottery are not coincident with the range of Nilo-Saharan languages, barbed bone points and the ranges of selected water-dependant species that we postulate the Nilo-Saharan peoples were hunting (e.g. alternate pivot-stamp pottery in Fig. S14).

Saharan pottery exhibits many different decorative styles that have been grouped into different characteristic motifs (70) (Fig. S14). However, it appears that in some cases similar motifs have been made with different tools (e.g dotted wavy line with either a comb or catfish spine) and thus it

11 is not yet clear if specific motifs represent developments by a specific cultural group or are an innovation that spread between groups (71), as is suggested by its rapid spread (68). Furthermore, linking pottery to the Aqualithic is complicated by the fact that different styles of pottery and stone tools have been found associated with barbed bone points and associated aquatic animal remains. This has led to criticism of the Aqualithic model for being associated with cultural heterogeneity rather than uniformity. We postulate that the rapid spread of pottery between groups with different lithic traditions (68) indicates that some technologies spread between different cultural groups, rapidly losing any spatial association with the ‘archaeological cultures’ that they originated within. Pottery perhaps achieved this because it could be adapted for multipurpose use. However, well- defined and more permanent cultural traditions appear to have been perpetuated through these ‘revolutions’, the Nilo-Saharan barbed bone point aquatic hunting tradition being a case in point. The bone point differing from pottery in that it was only useful for one specific activity, hunting large water-dependant animals.

Chronologically, the earliest barbed bone point records are in the Upper Semliki Valley in modern- day Democratic Republic of the Congo (72). This corresponds well with the spatial distribution of Nilo-Saharan languages, which are at their most diverse in the Ethio-Sudan borderlands, and thus appear to have originated there. The internal structure of Nilo-Saharan is given in Fig. S15, showing the two branches in the region of the Sahara under discussion are remote from the core area of diversity in the Ethio-Sudan borderlands. We hypothesise that the sudden abundance of aquatic fauna was responsible for the westward expansion of the phylum and the subsequent diversification into subgroups, thereby introducing barbed bone points in this region. Additional support for this comes from the potential to reconstruct both ‘hippo’ and ‘crocodile’ across significant ranges of Nilo-Saharan (Table S2 and 3).

7) Optically stimulated luminescence (OSL) dating of palaeolake sediments OSL samples were prepared using standard laboratory techniques. Briefly, carbonates and organic matter were removed from the sample using 1M HCl and H2O2. Coarse-grained samples were wet sieved to 180-212 µm while the fine silt fraction (4-11 µm) was extracted from fine-grained samples by Stokes settling. Pure quartz was extracted from the coarse fraction using density separations at 2.62 and 2.70 g/cm3 and a subsequent HF acid etch (23M HF for 40 min followed by an 10M HCl rinse). The fine silt fraction was agitated in 2.5M H2SiF6 for two weeks followed by a 10M HCl rinse. Refined quartz was deposited as a monolayer on aluminium discs using Silkospray silicone oil (180-212 µm) or by settling in deionised water (4-11 µm).

The single-aliquot regenerative-dose procedure (73) was applied to all samples using standard Risø TL/OSL readers fitted with blue (470Δ20µm) light emitting diode stimulation sources (74). Samples FZ9, 10, 11 and 72 were measured using preheat temperatures of 260°C for 10s prior to measurement of the natural/regenerated luminescence intensity (PH1), and 220°C for 10s prior to measurement of the (5 Gy) test dose luminescence intensity (PH2). An infra-red wash (60s at room temperature) prior to all OSL measurements (75) and a high temperature blue-diode bleach (280°C for 100s) after each test dose measurement (76) was incorporated into the basic SAR procedure (73). In contrast, samples NG 22 and 24 were measured using the preheat plateau approach (PH1 from 160-280°C in 20°C steps with a 160°C cut-heat for PH2) with no infra-red wash or high temperature bleach. This measurement regime was used for the Lake Megachad samples since they form part of a larger series, most of which are Holocene in age. The preheat plateau approach is useful when dating Holocene samples since it potentially allows detection of deleterious thermal transfer effects (e.g. Fig. 5 of ref. 77). To ensure that the two datasets are comparable, four Fezzan Basin samples (18) and two Lake Megachad samples were dated using both measurement regimes and in all cases the results for individual samples were indistinguishable within errors. All growth curves were fitted using a saturating exponential plus linear function. Recycling ratios were calculated to monitor the performance of the SAR procedure (73) while sample purity was assessed using the IR depletion ratio method (78). Aliquots not yielding recycling or IR depletion ratios consistent with unity were rejected. The sample equivalent dose was calculated as the unweighted mean of equivalent dose values obtained from aliquots yielding acceptable recycling and IR depletion ratios. Dosimetry data and age calculations are presented in Tables S4 and S5 respectively.

8) Supporting References 1. Van Damme D (1984) The freshwater mollusca of Northern Africa. Distribution, biogeography and palaeoecology (Developments in Hydrobiology, 25, Dr Junk publ., Hague). 2. Le Berre M (1989) Faune du Sahara Volume 1: poisons, amphibians, reptiles (LeChevalier~R. Chabaud, Paris). 3. Lévêque C (1990) Relict tropical fish fauna in central Sahara. Ichthyol Explor Freshwat 1: 39-48. 4. Doadrio I (1994) Freshwater fish fauna of North Africa and its biogeography. Ann Mus R Afr Centr Zool 275: 21–34.

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18 74. Bøtter-Jensen L, Bulur E, Duller GAT, Murray AS (2000) Advances in luminescence instrument systems. Radiation Measurements, 32: 523-528. 75. Olley JM, Pietsch T, Roberts, RG, (2004) Optical dating of Holocene sediments from a variety of geomorphic settings using single grains of quartz. Geomorphology 60: 337-358. 76. Murray AS, Wintle AG (2003) The single aliquot regenerative dose protocol: potential for improvements in reliability. Radiation Measurements, 37: 377-381. 77. Armitage SJ, Botha GA, Duller G.T, Wintle AG, Rebêlo LP, Momade FJ (2006) The formation and evolution of the barrier islands of Bazaruto and Inhaca, Mozambique. Geomorphology 82: 295-308. 78. Duller GAT (2003) Distinguishing quartz and feldspar in single grain luminescence measurements. Radiation Measurements, 37: 161-165. 79. Bender ML (1997) The Nilo-Saharan languages: a comparative essay (Lincom Europa, Munich).

9) Supporting Tables Supporting Table 1. Animals that show a trans-Saharan species distributions.

(A) Green Sahara (B) Nile Corridor (C) North and South Fish Tilapia zillii* Tilapia zillii* - Clarias gariepinus* Clarias gariepinus* - Hemichromis letourneauxi * Hemichromis letourneauxi * - Raiamas senegalensis* Raiamas senegalensis* - Molluscs Melanoides tuberculata* Melanoides tuberculata* Unio elongatulus Ancylus fluviatilis Lymnaea natalensis Pisidium casertanum Afrogyrus coretus Bulinus truncates* - Bulinus truncates* - - Reptiles Spalerosophis diadema Naja haje Malpolon moilensis Bitis arietans Trachylepis quinquetaeniata Telescopus obtusus Echis leucogaster - Lamprophis fuliginosus Stenodactylus petriei - Mauremys leprosa Tropiocolotes steudneri - - Tropiocolotes tripolitanus - - Acanthodactylus boskianus - - Mesalina olivieri - - Scincopus fasciatus - - Mammals Taphozous nudiventris - Paraechinus aethiopicus Nycteris thebaica - Crocidura lusitania Rhinolophus clivosus - Suncus etruscus Hipposideros caffer tephrus - Rhinopoma microphyllum Pipistrellus kuhli - Rhinolophus blasii Tadarida aegyptiaca - Nycticeius schlieffeni Mellivora capensis - Genetta genetta Hystrix cristata - Total 25 9 13 • exhibits more than one spatial distribution.

(A) Green Sahara: Animals that could have crossed the Sahara without using the Nile corridor. They are found north and south of Sahara with refuges in the middle suggesting prior dispersal with subsequent local isolation of intermediate populations. (B) Nile Corridor: Animals that occupy the Nile corridor and are found both north and south of the Sahara. These species could have used the Nile corridor to cross the Sahara. (C) North and South: Animals found both north and south of the Sahara but not in the middle. This distribution indicates prior dispersal across the Sahara with subsequent extinction of Saharan populations. No migration route can be attributed to species displaying this distribution.

Supporting Table 2. Cognate words for ‘hippo’ in Nilo-Saharan languages. Family Subgroup Language Attestation Gumuz Kokit baŋa Maba Aiki bùngùr Central Sudanic Sara Nar Àbà Songhay Kaado Bàŋà Koyra ChiiniBaŋa

Supporting Table 3. Cognate words for ‘crocodile’ in Nilo-Saharan languages. Family Language Attestation Attestation Koman Uduk ànàŋà Kuliak Ik nyeti-nyáŋ Eastern Sudanic Proto-Nilotic aaŋ Eastern Sudanic Gaam aaŋ Maba Aiki gòrndí Saharan Kanuri kárám Songhay Zarma kààrày

Supporting Table 4. Dosimetry data for OSL ages presented in this study. Radioisotope concentrations were measured using ICP-MS (U and Th) and ICP-AES (K). The calculation of the cosmic ray dose rate is based on the sample depth and an assumed overburden density of 1.85g/cm3. Sample Site Radioisotope concentrations Burial depth Cosmic dose rate K (%) U (ppm) Th (ppm) (m) (Gy/ka) Ages presented in Fig. 4a NG22 Kawiya ridge 0.68 ± 0.07 1.42 ± 0.14 7.75 ± 0.78 4.85 ± 0.2 0.11 ± 0.00 NG24 Alhajiri ridge 1.22 ± 0.12 1.34 ± 0.13 9.48 ± 0.95 4.4 ± 0.2 0.12 ± 0.00 Ages presented in Fig. 4b FZ9 Wadi ash Shati 0.61 ± 0.06 1.82 ± 0.18 8.26 ± 0.83 1.7 ± 0.2 0.18 ± 0.00 FZ11 Wadi ash Shati 0.54 ± 0.05 3.73 ± 0.37 5.72 ± 0.57 2.15 ± 0.2 0.17 ± 0.00 FZ12 Wadi ash Shati 0.60 ± 0.06 3.79 ± 0.38 4.62 ± 0.46 1.05 ± 0.2 0.19 ± 0.01 FZ72 Wadi el-Agial 0.63 ± 0.06 3.60 ± 0.36 6.94 ± 0.69 1.6 ± 0.2 0.18 ± 0.01

21 Supporting Table 5. Calculation of OSL ages presented in this study. Uncertainties are based on the propagation of errors associated with individual errors for all measured quantities. In addition to uncertainties calculated from counting statistics, errors due to (1) beta source calibration (3%), (2) ICP-MS/AES calibration (3%), (3) dose rate conversion factors (3%) and (4) attenuation factors (2%) have been included. Sample Site Water content Dose rate OSL sample grain Equivalent Age size (µm) dose (Gy) (%) (Gy/ka) (ka) Ages presented in Fig. 4a NG22 Kawiya ridge 5 ± 5 1.48 ± 0.08 180-212 186 ± 13 125 ± 12 NG24 Alhajiri ridge 5 ± 5 2.04 ± 0.12 180-212 233 ± 24 114 ± 14 Ages presented in Fig. 4b FZ9 Wadi ash Shati 7 ± 5 1.84 ± 0.10 4-11 180 ± 7 97.7 ± 6.5 FZ11 Wadi ash Shati 7 ± 5 2.13 ± 0.13 4-11 227 ± 8 107 ± 8 FZ12 Wadi ash Shati 7 ± 5 2.15 ± 0.14 4-11 233 ± 12 108 ± 9 FZ72 Wadi el-Agial 5 ± 5 1.92 ± 0.09 180-212 228 ± 16 119 ± 10

10) Supporting Figures

Supporting Fig. 1. Landsat Thematic Mapper false colour composite image of the Darfur Fan in Sudan that links the Nile and Chari rivers and thus explains the similarity in their aquatic biodiversity. (A) The Darfur Fan catchment area. (B) A detailed image of the fan. C) The area shown in SF2.

Supporting Fig. 2. Landsat Thematic Mapper false colour composite image of the Darfur Fan in flood on the 8th of September 1986. Blue colours are water and two active channel systems are evident, one on the western side of the fan and one on the eastern side.

Supporting Fig. 3. (A) DEM and palaeo-hydrological interpretation of the Niger Delta, the Erg of Azaoud and the Tanezrouft Fan during the Late Pleistocene and Early Holocene. Red arrows indicate the location of the bifurcation points that feed waters from the mountains in different directions. The Black rectangle outlines the region shown in B. (B) DEM and palaeo-hydrological interpretation of the Niger Delta region during the Middle Holocene. The entire fan is covered in palaeo-channels thus only the currently active channels and the large palaeo-channels have been marked. Lake Debo is much smaller than shown in A. The size shown here is its historical size when the Niger is in Flood. The possibility of a much larger lake during the Early Holocene is shown in A as discussed by McIntosh (30).

Supporting Fig. 4. Possible hydrological connection between the Ahnet-Mouydir Basin (west side of fault) and the Chotts Basin (east side of fault).

Supporting Fig. 5. Late Pleistocene and Early Holocene palaeo-hydrology of the Sahara (~11-8 ka). Boundaries between the main biogeographic provinces for the African mollusc species are indicated along with the distribution of Melanoides tuberculata, both recently as indicated by the hatched area and the marked Saharan refuges as well as during the Holocene by marking the location of fossils. A trans-Sahara distribution is evident, both across the Sahara and down the Nile. Note that the province Ethiopian 2A corresponds closely both with the fish biogeographical province of the Sahara and the trans-Saharan interconnected waterway.

Supporting Fig. 6. Late Pleistocene and Early Holocene palaeo-hydrology of the Sahara (~11-8 ka) with the boundaries between the main biogeographic provinces for the African amphibian species indicated along with the current distribution of the toads Bufo viridis and Bufo xeros as indicated by the hatched area and the marked Saharan refuges. The distribution of these two toads suggest that when the Sahara was more humid Bufo xeros moved north Bufo viridis moved south and they met in the middle.

Supporting Fig. 7. Late Pleistocene and Early Holocene palaeo-hydrology of the Sahara (~11-8 ka) with the boundaries between the main biogeographic provinces for the African amphibian species indicated along with the current distribution of the frogs Rana saharica and Hoplobatrachus occipitalis as indicated by the hatched area and the marked Saharan refuges. The distribution of these two frogs is similar to that of toads and suggest that when the Sahara was more humid Hoplobatrachus occipitalis moved north Rana saharica moved south and they met in the middle.

Supporting Fig. 8. Late Pleistocene and Early Holocene palaeo-hydrology of the Sahara (~11-8 ka) with the fish biogeographic provinces. The current distribution of catfish (Clarias gariepinus and Clarias anguillaris) is also indicated by the hatched areas and the Saharan refuges marked with coloured dots. The Holocene distribution is shown by marking the location of Holocene fossils. For Clarias gariepinus a trans-Sahara distribution is evident, both across the green Sahara and down the Nile.

Supporting Fig. 9. Late Pleistocene and Early Holocene palaeo-hydrology of the Sahara (~11-8 ka) with the distribution of Crocodylus niloticus indicated, both historically (~1900) as shown by the hatched area and during the Holocene by marking the location of rock art, fossils and historical reports (early Roman to 1900). A trans-Sahara distribution is evident, both across the green Sahara and down the Nile.

Supporting Fig. 10. Late Pleistocene and Early Holocene palaeo-hydrology of the Sahara (~11-8 ka) with the distribution of Giraffa camelopardalis indicated, both historically (~1900) as shown by the hatched area and during the Holocene by marking the location of rock art and fossils. A trans- Sahara distribution is evident, both across the green Sahara and down the Nile.

Supporting Fig. 11. Late Pleistocene and Early Holocene palaeo-hydrology of the Sahara (~11-8 ka) with the distribution of Loxodonta africana indicated, both historically (~1900) as shown by the hatched area and during the Holocene by marking the location of rock art, fossils and historical reports (early Roman to 1900). A trans-Sahara distribution is evident.

Supporting Fig. 12. Late Pleistocene and Early Holocene palaeo-hydrology of the Sahara (~11-8 ka) with the distribution of Lates niloticus indicated, both currently as shown by the hatched area and during the Holocene by marking the location of fossils. A distribution restricted to the River Nile and the southern-central Sahara is evident.

Supporting Fig. 13. Late Pleistocene and Early Holocene palaeo-hydrology of the Sahara (~11-8 ka) with the distribution of Mollusc biogeographic provinces and the location of species requiring long term water connections (Bellamya unicolor, Cleopatra bulimoides, Pila and Lanistes as suggested by (1). A distribution restricted to the River Nile and the southern-central Sahara is evident.

Supporting Fig. 14. Late Pleistocene and Early Holocene palaeo-hydrology of the Sahara (~11-8 ka) with the spatial distribution of dotted wavy line and alternate pivot-stamp pottery plotted (from Ref. 70).

Proto-Nilo-Saharan

Songhay Saharan Kuliak Satellite-Core Group

Maba For Central Sudanic Berta Kunama Core

East Sudanic Koman Gumuz Kado

Supporting Fig. 15. The internal structure of Nilo-Saharan with Songhay and Saharan languages as geogrpahic and genetic outliers (79).

Supporting Fig. 16. Digital elevation models showing the location and age of MIS5 lacustrine deposits (A) Pleistocene beach ridges of Lake Megachad, (B) Fezzan Basin. The location of MIS5 lakes in the Fezzan Basin are indicated in blue, while the black lines show the location of the rivers that feed them, the thin grey line their probable extension under the dunes and the thick grey line the catchement area of the Fezzan Basin.