Disjunct distributions of freshwater snails testify to a central role of the Congo system in shaping biogeographical patterns in Africa
© Schultheiß et al.; licensee BioMed Central Ltd. 2014
Received: 18 November 2013
Accepted: 27 February 2014
Published: 6 March 2014
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. 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.
We study these biogeographical patterns using a fossil-calibrated multi-locus phylogeny of the gastropod family Viviparidae. This group allows reconstructing drainage patterns exceptionally well because it disperses very poorly in the absence of existing freshwater connections. 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.
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. 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. Finally, we review similarities and differences in patterns of vertebrate and invertebrate dispersal. 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.
KeywordsFreshwater biogeography East African Rift System Congo Lake Malawi Lake Tanganyika Zambezi
The formation of the East African Rift System (EARS) played a decisive role in the evolution of Africa’s tropical fauna and flora. 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. Rifting created, disrupted, redirected, and connected major freshwater systems .
Most suggestions of palaeohydrological connections in tropical Africa are based on circumstantial evidence in combination with general models of rifting and uplifting  rather than on geomorphological evidence like in other parts of the continent where palaeochannels can be traced over considerable areas and are reasonably well dated, e.g. [5–7]. The consequential lack of a coherent synthesis or a model of hydrographical connections since the Mid-Miocene severely hampers our understanding of historical biogeography in tropical Africa. This is further complicated by a scarcity of samples from the Congo River system, e.g. [8–11], but see Goodier et al.  and Day et al. . The Congo is the largest freshwater system in the centre of the continent and palaeohydrological research indicates that the river and its tributaries have a highly vicissitudinous drainage history. Temporal connections existed to the present day Lake Victoria area [14, 15], Lake Turkana [16, 17], the Upper Zambezi area [18, 19] and the Indian Ocean , although the latter connection is controversial . Hence, the analysis of Congolese samples is a prerequisite for our understanding of the evolution and distribution of the freshwater fauna of tropical Africa—including the origins of the endemic radiations in the rift-lakes Malawi and Tanganyika.
Here we study the historical biogeography of the freshwater gastropod family Viviparidae, a taxon widely distributed in the lotic and lentic environments of tropical Africa . This family is of particular interest to studies of historical freshwater biogeography because its dispersal is mostly limited to habitats with existing freshwater connections , rendering it an ideal tracer of past and present hydrographic connections. The ovoviviparous and dioecious reproduction mode of viviparids minimizes opportunities for successful vector-mediated migration and a subsequent establishment of a viable population [22, 23]. Accordingly, viviparid fossils are conspicuously absent from African water bodies that were never hydrographically connected to a source, e.g. crater- and oasis lakes .
We obtained samples from the major drainage systems in the region, i.e. that of the Nile, the Okavango, the Zambezi as well as the Upper and Middle Congo. Using Bayesian multi-locus phylogenetic analyses and a fossil-calibrated, relaxed molecular clock we studied the diversification and distribution of viviparids in Africa. In light of the impact of the evolution of the EARS on African hydrographic systems and the dependence of our model organism on these systems to disperse, we expect a deep phylogenetic separation between viviparid species east and west of the western branch of the rift system. We furthermore hypothesize this separation to temporarily coincide with the disruption of freshwater migration routes across the evolving rift.
The phylogenetic structure revealed by Figure 2 also indicates that morphological identifications and genealogy do not match each other perfectly. A main concern is the systematic position of Bellamya capillata, which has been traditionally reported from many localities in Africa south of the equator . The type locality for this taxon is Lake Malawi, and all other localities from which the species was identified, are in fact inhabited by populations that are deeply divergent from B. capillata in Lake Malawi. Similar issues exist for other Bellamya species (see Discussion). We thus tentatively name specimens with an ambiguous status in current systematics using ‘confer’ (cf.) to emphasize that taxonomic revisions are required.
Molecular clock estimates
We focus on estimates for the ages of the following three nodes in Clade I (Figure 2): Split A—most recent common ancestor (mrca) of the entire clade: 10.47 million years (My) (95% confidence interval [CI]: 6.69-15.04 My); Split B—the split between the Victoria- and the Okavango group: 6.32 My (CI: 3.58-9.96 My); Split C—the split between the Congo- and the Malawi group: 4.52 My (CI: 2.32-7.70 My). The age of the mrca of the Southern group in Clade II is 1.916 My (CI: 0.88-3.31 My). Note that the here estimated mean substitution rate of the COI fragment is 0.93% per My (CI: 0.68-1.18) and therewith very similar to the trait-specific COI Protostomia clock rate for the HKY model suggested by Wilke et al.  for dioeceous tropical and subtropical taxa with a generation time of 1 year and a body size of approximately 2–50 mm (mean rate: 1.24% per My; CI: 1.02-1.46). Substitution rates are provided in Additional file 1 for each fragment.
In order to explain our findings we integrated our phylogenetic information with literature data on palaeohydrographical connections to provide a synthesized, spatially and temporarily explicit model of historical freshwater biogeography in tropical Africa. Subsequently, we review recently published studies on African fish biogeography and evaluate similarities and dissimilarities of vertebrate and invertebrate dispersal patterns.
Historical biogeography of Bellamyain tropical Africa
The earliest African viviparid fossils were found in tropical regions  (Additional file 2). We thus assume that this region is the geographical origin of an ancestral population of Clade I in the Middle/Late Miocene (~12 Ma; Figure 3-1).
Subsequently this ancestral lineage split into the Congo-Malawi- and the Victoria-Okavango-cluster (Split A in Figures 2 and 3-2; mean age ~10.5 My). In the Late Miocene/Early Pliocene the waters of the present day Lake Victoria region drained via a precursor of the Aruwimi River into the Congo [14, 15]. A contemporaneous connection from the Congo system to the headwaters of the Upper Zambezi was suggested via the Kasai River [19, 28, 29], which served as a dispersal route for various fish taxa [11, 12, 30, 31]. This persistent freshwater connection likely also enabled viviparid migration between the present day Lake Victoria region and the Upper Zambezi/Okavango watershed (Figure 3-2). We postulate that contemporaneously the Congo-Malawi-cluster inhabited the Upper Congo catchment including the Chambeshi system—which drained eastward into the Rufiji system until the Pliocene —, the emerging Lake Malawi, and perhaps Palaeolake Rukwa  (Figure 3-2). At that time no hydrographical connection existed between the Upper and the Middle Zambezi [28, 33, 34] and there was no faunal exchange between the Victoria-Okavango-cluster and the Congo-Malawi-cluster.
In the Late Miocene/Early Pliocene the Okavango group started to separate from the Victoria group (Split B in Figures 2 and 3-3; mean age ~6.3 My). During a wet phase in East Africa around 3.0-2.8 Ma faunal elements of Congolese origin (e.g. molluscs and sponges) colonised the Turkana Basin for the last time and all subsequent invasions into the basin were of Nilotic origin [16, 17]. This data indicates that the connection of the Victoria region to the Central Congo ceased, at latest with the closure of the Beni Gap in the Early Pleistocene  but perhaps earlier ; a similar timeframe is assumed for the disruption of the Okavango/Upper Zambezi-Congo connection [3, 28, 35]. We argue that the final separation of the two groups was ultimately governed by these events (Split B in Figure 2) but we acknowledge that the confidence interval for Split B also allows for an earlier separation. Around this time, the ancestors of the current Congo-Malawi groups inhabited an area encompassing the Upper Congo system, the Chambeshi system, and young Lake Malawi, most likely using the northwest corner of the lake’s basin as gateway [3, 19] (Figure 3-3).
Subsequently the connection between Lake Malawi and the Chambeshi/Upper Congo system ceased, which separated the Congolese from the Malawian Bellamya (Split C in Figures 2 and 3-4; mean age ~4.5 My). This faunal disruption may have been a direct consequence of rifting in the Mweru-Mweru Wantipa fault zone and in the northern part of the Malawi Rift [36–38]. The extant viviparid fauna of the lakes Mweru and Bangweulu is however no remnant of this former Congo-Malawi-cluster (Figure 2). In fact, age and phylogenetic position of the Mweru/Bangweulu viviparids suggest a re-colonization of the two lakes from the Zambezi via the Kafue River , perhaps after a climatically-induced Pleistocene ecosystem crisis comparable to those in nearby Lake Malawi in the east [40–42] and Lake Palaeo-Makgadikgadi to the west . Moreover, the polyphyletic pattern of the Mweru/Bangweulu viviparids indicates that the two lakes may have been colonized multiple times from the Zambezi River system (Figures 2 and 3-4). In the Late Pliocene/Early Pleistocene the Upper Zambezi was captured by the Middle Zambezi [28, 34], which enabled secondary contact between the Okavango group and Clade II (Figures 2 and 3-4). The observable geographical overlap between the two groups coincides with the area of Lake Palaeo-Makgadikgadi, which existed in consecutive phases over the Middle and Late Pleistocene [43–45] (Figures 1 and 3-4). This lake may have stirred populations of initially different geographic origin (e.g. the Okavango group and Clade II) and, hence, superimposed previous spatial patterns resulting in the current overlapping distributions of Bellamya groups.
The phylogeny presented here reveals an unanticipated sister relationship of Lake Malawi’s extant Bellamya fauna to that of the Middle Congo. In light of the well-supported reciprocal monophyly of both groups we argue that the separation of the Congo-Malawi-cluster (Split C in Figures 2 and 3-4) was a consequence of the disruption of hydrological connections and therewith migration routes (e.g. due to rifting processes) rather than of dispersal from the Congo River system into Lake Malawi or vice versa. Dispersal would most likely have resulted in a pattern where the sink population is nested within the paraphyletic source population instead of the observed reciprocal and strict regional monophyly. The Bellamya of the lakes Mweru and Bangweulu, which re-colonized these water bodies from the Zambezi system, illustrate such a case of dispersal (Figure 2). We hence also conclude that the general dominance of regionally confined monophyletic clusters in our dataset points toward a prevalence of vicariance over dispersal processes in the historical biogeography of the taxon—in contrast to, e.g., some fish taxa (see below).
Viviparid fossils with an age of up to four million years are reported from the Chiwondo Beds in the Northwest of the Malawi Basin . Because the mean age of the split between the Malawi and the Congo group is of a similar age, our results do neither reject the possibility of an uninterrupted evolutionary Bellamya lineage in Lake Malawi (the founder-flush model in Schultheiß et al. [47, 48]) nor the possibility that the lake was re-colonized after its Pliocene fauna went extinct, e.g. during severe lake level low stands . In any case, the onset of molecular diversification of the modern endemic Malawi group started considerably later (1.39 Ma; CI: 0.56-2.61 My) than the deposition of the Plio-Pleistocene Chiwondo Bed fossils. Thus it has paralleled the diversification of the endemic Lanistes taxa of Lake Malawi .
Although Neothauma is currently endemic to Lake Tanganyika, this has not been the case from the Late Miocene to the Early Pleistocene when the genus radiated in Palaeolake Obweruka . This palaeolake occupied the Lake Albert-Edward region and was similar in size and depth to Lake Tanganyika prior to the uplift of the Rwenzori Mountains ~2.3 Ma [14, 49]. The molecular phylogeny indicates that the Neothauma lineage from Lake Tanganyika evolved fairly isolated from the African Bellamya (Figure 2). A similar spatial, temporal, and genetic distinctness is reported for some fish taxa of Lake Tanganyika [31, 50, 51]. It appears reasonable to assume that the lake served as a refuge and harbours the sole survivors of the formerly more widely distributed and morphologically diverse genus Neothauma. Moreover, the isolated evolutionary history of Lake Tanganyika’s viviparid fauna implies that for the timeframe and migration events discussed in this paper the lake served neither as a gateway nor as a dispersal route.
Comparative biogeography of afrotropical freshwater taxa
This paper is to our knowledge the first invertebrate study investigating patterns of historical freshwater biogeography in tropical Africa using molecular data. Against the background of recent studies on African fish biogeography we here review patterns of vertebrate and invertebrate biogeography with a strong focus on dispersal abilities, hybridization, and migration routes.
A striking difference between viviparid and fish patterns lies in the phylogenetic relationships of taxa from the modern Lake Victoria region: fish specimens from the Lake Victoria region cluster generally with other East African species, e.g. [31, 50, 52, 53]. In contrast, the sister-taxon relationship between viviparids from the Lake Victoria region and those from the Okavango/Upper Zambezi is to date unique among the afrotropical freshwater fauna. This pattern is remarkable because connecting these two drainage systems requires crossing two divides: (A) the Congo/Upper Zambezi water divide via a precursor of the Kasai River and (B) crossing the emerging western branch of the EARS. To provide a hypothesis as to the cause of the difference of biogeographical patterns between fish and viviparid taxa, we suggest that the rifting process was the vicariance event that caused the main phylogenetic separation of fish taxa into species east and west of the western branch of the EARS. At this stage, however, the afrotropical Viviparidae were already separated into the Congo-Malawi cluster and the Victoria-Okavango cluster (in the aftermath of Split A; Figures 2 and 3). We argue that this initial Split A was invoked by a migration barrier—perhaps in the Congo Basin—that inhibited viviparid dispersal yet allowed fish dispersal. Intrinsic biological properties may create differential abilities to overcome ecological, behavioural, and physical barriers , e.g. differences in mobility may cause differential migration through corridors which only exit during annual flooding. For example, two major flooding events since 2010 promoted the migration of fish from the Okavango Delta into the formerly dry Boteti river bed. However, Bellamya—which lives in permanent overspills of the Okavango Delta such as the Thamalakane River—did not migrate into the Boteti River (FR pers. observation, 2010, 2011, and 2013).
Eventually, the rifting process separated the two viviparid clusters into the four modern groups (i.e. the Congo-, Malawi, Okavango-, and Victoria group; Splits B and C) subsequently to Split A. Each of these groups is (much like in fish) confined to one side of the western branch of the EARS.
This pattern and comparative biogeography sheds new light on freshwater migration corridors over the emerging rift. African tigerfish, for example, were suggested to have migrated during the Late Miocene along an east–west corridor from the Tanzanian Rufiji-Ruaha system via the Luangwa to the Upper Zambezi and the Okavango , crossing the young rift at the narrow Rukwa-Rungwe region prior to the uplift of the Ufipa plateau . A similar corridor over the rift appears to have been feasible for mastacembelid eels  and, in fact, also for viviparids: The Congo-Malawi-cluster would likewise have occupied the Rukwa-Rungwe region (green area in Figure 3-2). It would hence be highly improbable that members of the Victoria-Okavango cluster migrated contemporaneously from the Victoria region through this corridor across the Rukwa-Rungwe area into the Upper Zambezi/Okavango. This would imply that members of this cluster migrated along the same hydrographical system as the members of the Congo-Malawi-cluster, yet without disrupting the here revealed biogeographical pattern. Consequently, we suggest the existence of a second east–west migration corridor (red area in Figure 3-2) connecting the Victoria region with the Okavango/Upper Zambezi area.
With the exception of some branches in Clade II, our phylogeny generally features strict regional monophyly—a pattern often absent in biogeographical studies of fish in tropical Africa, e.g. [11, 12, 55]. This absence is generally attributed to hybridization and active, long distance dispersal, e.g. [8, 11, 12, 31, 52], which hence appear to have played only a minor role in the historical biogeography of viviparids. Therewith, superimposition of underlying distributional patterns by recent active dispersal or hybridization seems negligible for this gastropod group, which in turn facilitates the reconstruction of original migration corridors.
The decisive phylogenetic pattern notwithstanding, further sampling is required to substantiate the proposed model. In particular, more sampling from the central Congo area is desirable despite logistic challenges, e.g., to search for putative remnants of the Victoria-Okavango-cluster (red dashed area in Figure 3-3). Furthermore, specimens are required from the Rufiji-Ruaha system to test our hypotheses associated with the Malawi-Congo-cluster (green dashed area in Figure 3-3). Eventually, more comprehensive sampling of the Lower Zambezi may shed light on the origins and evolution of Clade II. It is noteworthy that such an extension of the dataset will also enable a systematic revision of the genus Bellamya, as our work reported considerable incongruences between traditional taxonomy and the results of molecular phylogenetic analyses, e.g. [47, 56].
We have presented a first integrated model of historic freshwater invertebrate biogeography in tropical Africa. By comparing our results to fish data we demonstrate the importance of broad geographical and taxonomic sampling encompassing taxa with different dispersal abilities and life history traits. Our analysis shows that the biographical history of viviparids in tropical Africa is driven by consecutive vicariance events rather than by dispersal and is closely linked to the formation of the EARS. Moreover, we demonstrate that the Congo drainage system plays a central role in the distribution of the continent’s freshwater fauna during the late Cenozoic. Our data also sheds new light on the geographic origin of the endemic fauna of Lake Malawi and reveals its close phylogenetic relationship to Congolese populations. We hope that future work, with a further inclusion of invertebrate taxa, will help to refine our understanding of biogeographical patterns of tropical Africa’s freshwater fauna.
Sampling and species identification
Locality details and NCBI GenBank accession numbers of the specimens analysed in this study
B. cf. capillata
B. cf. capillata
B. cf. capillata
B. cf. capillata
B. cf. capillata
B. cf. capillata
B. cf. capillata
B. cf. unicolor
B. cf. capillata
B. cf. capillata
B. cf. capillata
B. cf. capillata
B. cf. monardi
B. cf. monardi
B. cf. capillata
B. cf. capillata
B. cf. capillata
B. cf. capillata
B. cf. capillata
B. cf. capillata
DNA extraction and amplification
We used a CTAB protocol for DNA extraction  and amplified four DNA fragments: the cytochrome oxidase subunit I (COI) with universal  and specific primers , the mitochondrial large subunit of ribosomal RNA (LSU rRNA) , a fragment of the nuclear LSU rRNA , and the nuclear histone 3 . PCR conditions were as given in  and sequencing was performed on an ABI3730XL sequencer (LGC Genomics Germany, Berlin). Sequences of all fragments were aligned unambiguously with ClustalW 1.4  in BioEdit 7.1  and checked by eye.
Phylogenetic analyses and molecular clock estimations
We ran five independent Bayesian phylogenetic reconstructions (partitioned into the four DNA fragments) in BEAST 1.75  to ensure convergence on the same posterior probability distribution. An unlinked HKY + Γ substitution model was utilized because more complex models showed indications of overfitting in preliminary runs; as tree prior we used a Yule model. In order to estimate divergence times we employed a fossil-based calibration using the earliest bellamyinid viviparid from Africa and the oldest Neothauma fossil (for an in-depth discussion see Additional file 2). The oldest Bellamya occurs in the Iriri Member of the Napak Formation at Napak and is ~19 My old . To implement this calibration point, we used a uniform prior over the root of the phylogeny spanning 23–13 My to account for dating uncertainty and the various published hypotheses as to when the Bellamyinae invaded Africa from Asia, e.g. [66–68]. The oldest Neothauma fossil (Neothauma hattinghi Van Damme & Pickford, 1999) is reported from the Upper Miocene Kakara Formation from the western branch of the East African Rift System and is 10–11 My old [15, 69]. For this second calibration point we used a normally distributed age prior (mean age: 10.5 My, standard deviation: 0.5 My) over the basal node leading to the monophyletic Neothauma clade (i.e. stem calibration in BEAST 1.75). Uncorrelated lognormal relaxed clock models were chosen to account for lineage specific rate heterogeneity within each partition; mixing of the Markov chains was monitored with Tracer 1.5 .
Ancestral area/state reconstructions as implemented in, e.g., Lagrange, BEAST and Mesquite are not feasible with the present datasets for two reasons. First, the basal topology of the African viviparids is unresolved, whereas a dichotomy is needed to reconstruct the ancestral state and the dichotomy-enforcing algorithm of BEAST would result in low node supports. Secondly, the four major groups of Clade I (Malawi, Congo, Okavango, and Victoria group) form a dichotomous topology (Figure 2), resulting in non-informative ancestral state reconstructions for Split C (Malawi/Congo) and Split B (Okavango/Victoria), and an ambiguous state reconstruction for the most basal Split A due to lacking information (unresolved topology) of the most common recent ancestor.
Availability of supporting data
The data sets supporting the results of this article are available in the treeBASE repository, http://purl.org/phylo/treebase/phylows/study/TB2:S15381.
All DNA sequences used in this study are available from NCBI GenBank. Accession numbers are provided in Table 1.
East African Rift System
Bayesian posterior probabilities
Most recent common ancestor
Cytochrome oxidase subunit I
- LSU rRNA:
Large subunit of ribosomal RNA.
We are grateful to Andrew Goudie, Jacek Stankiewicz, and Woody Cotterill for an evaluation of the model. Daniel Engelhard, Thies Geertz, Andreas Schumann, Jean-Papy Mongindo, Ernest Tambwe, Martin Pickford, Ezra Mussime and Kitam Ali are thanked for support in the field and access to museum specimens. Romy Richter, Catharina Clewing, and Silvia Nachtigall provided assistance in the laboratory. The manuscript benefited from careful readings by Woody Cotterill, Thomas Wilke, Gene Hunt, and two anonymous reviewers. The study was funded by the DFG projects AL 1076/5-2, AL 1076/6-2, RI 1738/3-1, and RI 809/20-1,2. BVB is a Peter-Buck Fellow of the Smithsonian Institution; his fieldwork related to the present study was funded by the Flanders Research Foundation and the Boyekoli Ebale Congo 2010 expedition through the Belgian Federal Directorate General for Development Cooperation (DGDC) and the Belgian Science Policy (BELSPO).
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