# Reconstructing the freshwater paleoecosystems diversity of Toros-Menalla (Late Miocene, Chad) from an integrated faunal perspective

Axelle Gardin, Olga Otero, Géraldine Garcia, Clarisse Nekoulnang, Fabrice Lihoreau, Abderamane Moussa, Mathieu Schuster, Lorenzo Scribano, Franck Guy

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Axelle Gardin, Olga Otero, Géraldine Garcia, Clarisse Nekoulnang, Fabrice Lihoreau, et al.. Reconstructing the freshwater paleoecosystems diversity of Toros-Menalla (Late Miocene, Chad) from an integrated faunal perspective. 2026. hal-05451106

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Reconstructing the freshwater paleoecosystems diversity of Toros-Menalla (Late Miocene, Chad)
from an integrated faunal perspective

Axelle Gardin¹,², Olga Otero², Géraldine Garcia², Clarisse Nekoulnang³, Fabrice Lihoreau¹,
Abderamane Moussa⁴, Mathieu Schuster⁵, Lorenzo Scribano¹, Franck Guy².

(1) ISEM, Université de Montpellier, CNRS, IRD, Montpellier, France

(2) Laboratoire PALEVOPRIM (UMR 7262 CNRS – Université de Poitiers), Poitiers, France

(3) Centre National de Recherche pour le Développement, N’Djaména, Chad

(4) Département de Paléontologie, Université de N'Djaména, N'Djamena, Chad

(5) Institut Terre & Environnement de Strasbourg (UMR 7063 CNRS – Université de Strasbourg), Strasbourg, France

Contact: axelle.gardin@umontpellier.fr

Abstract

Aquatic environments are critical components of past ecosystems that shaped species distribution and survival. Yet in hominin-bearing fossil sites, they are often treated as uniform or poorly detailed elements of “mosaic” landscapes, failing to capture their ecological complexity. In the northern Chad Basin, the late Miocene Toros-Menalla area records vast perilacustrine systems where aquatic and terrestrial ecosystems were deeply interconnected. While terrestrial vertebrate assemblages have been well characterised as reflecting a heterogeneous landscape, the aquatic component remains poorly resolved. Variations in depositional settings, aquatic vertebrate diversity, stable isotope data, and field observations point to a more complex and dynamic network of freshwater habitats. An integrative study of aquatic and semi-aquatic vertebrate assemblages from five Toros-Menalla sites reveals distinct faunal structures reflecting different ecological preferences and depositional conditions, ranging from perilacustrine floodplains to swampy, vegetated, or marginal waters and large open waterbodies with current. These environments, distributed across several hundreds of meters up to 30 km, represent lateral habitat diversity rather than temporal succession, as most assemblages formed geologically instantaneously (except for TM266, where vertical mixing could be hypothesised). Comparison with the present-day Bol Archipelago on the northeastern shores of Lake Chad provides a suitable analogue for the Toros-Menalla paleoenvironment. There, interdunal water bodies of varying depth and connectivity create a dynamic network of aquatic habitats at a similar spatial scale. This study underscores the need for systematic, grid-based collection and sieving of fossils to capture representative aquatic biodiversity and structure, and to reconstruct freshwater paleoenvironments with greater ecological precision.

Keywords : freshwater vertebrates, paleoecosystems, paleoecology, taphonomic and sampling biases,
assemblage analysis

Highlights

* Freshwater vertebrate assemblages differ across Toros-Menalla sites.

* These assemblages reveal a spatially diverse network of aquatic paleoenvironments.

* The Bol Archipelago offers a modern analogue for the Toros-Menalla aquatic paleoenvironment.

* Grid-based fossil collection is key to reconstructing freshwater paleoenvironments.
# 1. Introduction

Aquatic environments are critical components of past ecosystems, as they link biological, geological, atmospheric, and hydrological processes, thereby shaping species distribution and survival (e.g. Redfern et al., 2005; Davis et al., 2013; Dahlin et al., 2021). Yet, in hominin sites, they are often overlooked or overly simplified, either treated as a uniform landscape element or as part of a “mosaic”, which fails to capture their fine-scale ecological complexity and dynamics, especially when compared to terrestrial environments (e.g., Joordens et al., 2009; Otero et al., 2010, 2011; Cuthbert et al., 2017; Gibert et al., 2022; Gardin et al., 2024; Su, 2024).

In the northern Chad Basin, the Toros-Menalla area preserves hundreds of fossil sites that yielded a rich Late Miocene vertebrate fauna, including the earliest known hominin to date, *Sahelanthropus tchadensis* (Vignaud et al., 2002; Brunet et al., 2002, 2005). These sites document a landscape where terrestrial and aquatic ecosystems were deeply interconnected, within a vast perilacustrine system (Schuster 2006; Schuster et al., 2009; Moussa et al., 2016, 2021).

While terrestrial vertebrate assemblages from Toros-Menalla have been more studied, revealing a heterogeneous environment combining xeric to humid mixed/grasslands, palm groves, and forest patches (Le Fur et al., 2009, 2014; Blondel et al., 2010; Novello, 2012; Novello et al., 2015, 2017), the aquatic component remains poorly resolved. Variations in depositional settings, the diversity of aquatic and semi-aquatic vertebrates, stable isotope data, and field observations instead point to a complex and dynamic network of freshwater habitats (Otero et al., 2010, 2011) and depositional environments (Schuster et al., 2009; Le Fur et al., 2009, 2014; Moussa et al., 2021). Despite this evidence, aquatic environments at Toros-Menalla still lack a comprehensive and integrated faunal perspective that accounts for taphonomic and sampling biases. Such a framework is needed to characterise fine-scale paleolandscape heterogeneity and to meet the current challenge of resolving hominin environments at the local scales (Su, 2024).

To address this gap, we analysed freshwater-dwelling vertebrate assemblages (fishes, testudines, crocodilians, hippopotamuses, and anthracotheres) from five well-sampled sites. These sites were selected for their sampling quality, including small-mesh screening to capture substantial ichthyological diversity (Otero, 2010; Otero et al., 2010), and for the availability of material collected by specialists of the freshwater-dwelling vertebrate groups. First, the assemblages' structure and composition were compared. Then ecological factors that shape these assemblages have been explored, such as habitat preferences and ecological tolerances. Fossil preservation indicators helped infer the energy of the transport of bones and depositional conditions. The results are contextualised with stable oxygen isotope data. Finally, Toros-Menalla's paleoecosystems are discussed in light of these new data and sedimentological evidence, to identify a modern analogue that better reflects landscape dynamics, ecology, and site formation processes.

# 2. Material and Methods

## 2.1 Study Area and Geological Context

The Chad Basin is a vast intracratonic depression divided into two major sectors: the southern part, which hosts Lake Chad today, and the northern part, which lies more than 100 meters lower and is more exposed to aeolian deflation from the Sahara Desert (Fig. 1A). This northern sector has been repeatedly inundated since the Miocene by paleo-lakes referred to as “Megalake Chad”, with alternating phases of humid expansion and arid contraction. The most recent widespread highstand occurred during the Holocene (~6,000 years BP; Maley, 2004; Sepulchre et al., 2008; Schuster et al., 2005, 2009).

Located in this northern basin, the Toros-Menalla exposures show alternating giant cross-stratified sands, typical of dune deposits, and pelites and diatomites indicative of open lacustrine environments. Most vertebrate remains derive from a transitional sandstone attributed to a peri-lacustrine environment, recording episodic flooding and lake expansion during humid phases, alternating with recurrent desert episodes in the northern Chad Basin (Fig. 1C).
Fossils analysed in this study derive exclusively from the Anthracotheriid Unit, a sandy, around 4-meter-thick, fossil-rich layer within the Toros-Menalla sequence that also yielded abundant terrestrial fauna (Fig. 1C). This unit reflects peri-lacustrine to fluvial environments, including vegetated dunes, ephemeral ponds, paleosols, and ephemeral channels (Schuster et al., 2009; Moussa et al., 2021). Specimens from overlying diatomitic or clayey layers were excluded, as these represent open lacustrine settings and mainly yield isolated fish remains. The Anthracotheriid Unit was initially correlated with the Lower Nawata Formation at Lothagam (Kenya), dated between ca. 7.4 and 6.5 Ma (Vignaud et al., 2002; McDougall and Feibel, 2003). Subsequent radiometric dating places the unit between 7.46 ± 0.13 Ma (base) and 7.13 ± 0.14 Ma (top) at TM254, and between 7.34 ± 0.12 Ma (base) and 7.10 ± 0.14 Ma (top) at TM266 (Lebatard et al., 2010).

Since 1997, the Mission Paléoanthropologique Franco-Tchadienne (MPFT) has excavated over 14,000 catalogued vertebrate specimens from Toros-Menalla, including more than 4,000 aquatic and semi-aquatic remains. These include large semi-aquatic mammals (*Hexaprotodon garyam* Boisserie et al., 2005, *Libycosaurus bahri* Lihoreau et al., 2014), at least four crocodilian species, four semi-aquatic chelonians, and over twenty actinopterygian taxa (Otero et al., 2006–2011; Pinton et al., 2006, 2011, 2016, in review). These specimens were recovered from 262 fossiliferous sites. At Toros-Menalla, a “site” refers to the smallest spatially coherent unit identified in the field. In some cases, areas initially mapped as separate sites, often due to intervening dune ridges, actually represent a single one. Because our analyses focus on sites sampled under comparable protocols for aquatic vertebrates, such cases do not affect this study. Site size and configuration nevertheless vary considerably, ranging from a few square metres (TM337) to several hundred square metres (TM266).

## 2.2 Sampling Sites and Procedures

While large semi-aquatic mammals from Toros-Menalla have been extensively collected, other aquatic vertebrates, particularly ichthyofauna and herpetofauna, remain largely underrepresented in collections despite their abundance in the field. These discrepancies reflect long-standing sampling biases that can strongly affect paleoecological reconstructions. To address them, five sites (TM90, TM242, TM252, TM266, and TM337) were selected because they were sampled using consistent strategies and comparable effort for (semi-)aquatic taxa, ensuring reliable comparisons and representativeness. At these sites, fossils were recovered through both surface prospecting and grid-based sediment screening (1 × 1 m squares) targeting ichthyofauna, using a 1 mm mesh (2 mm at TM266). Assemblages from these sites therefore provide a robust representation of ichthyofauna and semi-aquatic mammals, and to a lesser extent semi-aquatic reptiles (Fig. S1). In addition to their sampling comparability, these sites were selected because previous studies and field observations suggested they represent distinct aquatic environments (Le Fur et al., 2009, 2014; Otero et al., 2011; Moussa et al., 2021; Otero pers. obs.).

The five sites lie within a maximum distance of 35 km, all located near the paleolake margin, within the broader Toros-Menalla fossiliferous area, which extends over ~200 km along its main east-west axis (Fig. 1B). TM242 and TM252 are only a few metres apart, and TM337 corresponds to a small fossiliferous zone adjacent to TM252. TM266 is the most distant site. The region is remarkably flat, with an estimated elevation difference of less than 5 meters between sites (Fig. 1).

## 2.3 Taxonomic and ecological grouping for inter-site comparison

This study is based on the paleontological collections curated at the CNRD (Centre National de Recherche pour le Développement, N'Djaména), including fish specimens recovered through grid-based screening at TM90, TM252, TM242, and TM337. Fossil specimens were identified to various taxonomic levels, most commonly at the genus or family level, although some were identified only at the class or order level, depending on preservation quality and the diagnostic value of the skeletal elements (Otero, 2010).

To ensure consistent and comparable assemblage composition and structure across sites, taxonomic grouping strategies were applied, as detailed below. Because ecological preferences are often poorly resolved for fossil species within certain genera (e.g., *Synodontis*, *Tetraodon*), and because taxonomic resolution varies between sites, specimens were grouped at the genus or family level to facilitate inter-site comparisons and minimise bias linked to uneven taxonomic identification (Table 1; Forcino et al.,
2012). Indeterminate specimens that could not be confidently assigned to these groups were excluded from the analysis. Based on preserved morphological information, these specimens likely belong to taxa already represented by better-preserved material, and their exclusion is therefore unlikely to reduce the ecological diversity captured in the dataset. For large semi-aquatic mammals, unidentified hippopotamid specimens in the catalogue were grouped under *Hexaprotodon garyam*, and unidentified anthracothere specimens were assigned to *Libycosaurus bahri*. This is justified by the current taxonomic consensus, which indicates the presence of a single hippopotamid species and a single anthracothere species at Toros-Menalla (Boisserie et al., 2005a, 2005b; Lihoreau et al., 2014). Although some specimens are not identified at the genus or species level, this reflects the non-diagnostic nature of the skeletal elements rather than true taxonomic diversity. Merging these specimens, therefore, avoids artificial inflation of ecological categories.

## 2.4 Testing sampling quality

To evaluate the sampling quality, rarefaction and extrapolation curves were computed using the iNEXT package in R 4.4.1 (Chao et al., 2014; Hsieh et al., 2016; R Core Team, 2024). After collecting between 160 and 270 specimens (depending on the site), fewer than one additional taxon is discovered with every extra 100 specimens (Fig. 2A). Given the higher number of specimens in the selected assemblages, the diversity of taxonomic groups of aquatic vertebrates is considered well-represented. Additionally, the sample coverage exceeds 98%, suggesting that further sampling at these sites is unlikely to reveal new taxa (Table 2).

## 2.5 Description of the assemblages

Multiple metrics were used to characterise the taxonomic composition and structure of the selected assemblages. For each taxonomic group, we report the number of specimens, the estimated minimum number of individuals (MNI), and standardised taxonomic rank abundance (see supplementary material). MNI was estimated based on the most abundant skeletal element, which varies among sites, taxa, and, when known, size classes. For fish taxa primarily represented by isolated teeth, MNI estimates were derived from tooth counts in modern analogues: 16 teeth for Alestidae indet. (e.g., *Brycinus*; Paugy, 2003), 20 for *Hydrocynus* (Paugy and Guégan, 1989), 10 for Labeo (Stewart and Murray, 2017), 50 for *Gymnarchus* (Bigorne, 2003), and four beak elements for *Tetraodon* (Lévêque and Paugy, 2003). We acknowledge, however, that the total number of teeth produced over an individual's lifetime cannot be precisely determined.

In addition to taxonomic diversity, we document available information on specimen taphonomy and site sedimentology. Relevant details on collection methods that may bias assemblage composition are also considered, as well as complementary data on paleodiversity when informative. These include the diversity and relative abundance of non-aquatic vertebrates, allowing a broader assessment of the relative contributions of aquatic and terrestrial habitats.

To improve comparability among sites with unequal sample sizes, standardised taxonomic rank abundance was calculated following Le Fur et al. (2014). This approach ranks taxa by abundance, with the most abundant taxon assigned the highest rank; ranks are then standardized by dividing by the total number of taxa at each site, accounting for differences in richness (Fig. 2B). Taxonomic abundances were calculated from MNI to limit biases linked to isolated teeth or scales that may derive from a single individual and artificially inflate abundance estimates.

## 2.6 Comparison of the assemblages

The similarity in taxonomic structure among sites was assessed using hierarchical cluster analysis based on the Bray–Curtis dissimilarity index in R (vegan package; Oksanen et al., 2022; R Core Team, 2024). This index quantifies differences in species composition and abundance, ranging from 0 (identical assemblages) to 1 (no taxa in common). To evaluate cluster robustness, multiscale bootstrap resampling was performed using the pvclust package (Suzuki and Shimodaira, 2006), providing two support metrics for each cluster: the approximately unbiased p-value (a.u. p-value) and the bootstrap probability (BP). Before clustering, abundance data were Hellinger-transformed to limit the influence of highly abundant taxa. Clusters with a.u. p-values >95% were considered strongly supported.
To further test differences in assemblage composition between predefined site groups, a permutational multivariate analysis of variance (PERMANOVA) was conducted using the adonis2() function in vegan. This approach evaluates whether between-group variation exceeds within-group variation.

# 3. Results

## 3.1 Similarity between assemblages

The most similar assemblages are TM252 and TM337 (Bray-Curtis similarity 79%; Fig. 3), likely due to TM337 being a small area nested within TM252. Both sites share many small bone fragments, small fish taxa (Alestinae, indeterminate Acanthomorpha), and one rare taxon (Mormyridae), with large semi-aquatic mammals being less abundant. However, TM337 has higher taxonomic diversity, including two additional rare taxa and a greater relative abundance of *Synodontis*. This cluster (TM252-TM337) is strongly supported by multiscale bootstrap resampling (a.u. p-value = 99%; Fig. 3), indicating a robust association in taxonomic composition.

TM90 and TM266 cluster together as well (similarity 64%, Fig. 3), likely due to their high taxonomic diversity among fishes and crocodilians, and the greater abundance of semi-aquatic reptiles and *Libycosaurus* individuals. However, TM90 is distinguished by an exceptional abundance of *Polypterus* and Clariidae, with many remains in anatomical connection, suggesting minimal transport. TM266, in contrast, is dominated by *Lates*, *Tetraodon*, and *Hydrocynus*, with well-preserved but mostly disarticulated remains, suggesting short-distance transport. The rare taxon *Heterotis* is also recorded at TM266. The TM90-TM266 cluster is moderately supported by bootstrap resampling (a.u. p-value = 93%).

TM242 is the most distinct assemblage (similarity from 59% to 69% with the four other sites), with the lowest taxonomic richness and an assemblage dominated by large semi-aquatic mammals (*Libycosaurus*, *Hexaprotodon*), Alestinae, and *Synodontis*. TM242 does not group robustly with any other site based on Euclidean distance (a.u. p-value < 95%), while it groups with the cluster TM252-TM90 based on Bray-Curtis dissimilarity index (Fig. 3).

However, grouping sites into three clusters (TM252-TM337, TM90-TM266, and TM242), the PERMANOVA test does not support the proposed clustering (F = 0.6419, p = 1.0), suggesting that the variation in taxonomic composition within clusters is comparable to the variation between clusters.

## 3.2 Descriptions and paleoecological interpretations

### 3.2.1 TM90

**Description.** Aquatic and semi-aquatic taxa represent 69% of the total number of specimens in the TM90 fossil assemblage, while terrestrial taxa account for 31% (Fig. 4). The assemblage includes 20 (semi-aquatic taxa and stands out from other sites due to the abundance of *Polypterus*, Clariidae, and *Libycosaurus* (Fig. 6). Among fishes, *Polypterus* is particularly abundant, with more specimens than at any other site in Toros-Menalla. Although most remains are scales, one nearly complete specimen and several body fragments show excellent three-dimensional preservation and attest the presence of many individuals (Fig. 5, Otero et al. 2006). Clariidae are also well represented and constitute the most abundant taxon in terms of individual counts at TM90 (Figs. 5, 6). The assemblage further includes small to very small unidentified Acanthomorpha (approx. 20 cm long), small Bagridae, and very large Claroteidae individuals. Other fish taxa are present but rarer, such as Cichlidae, *Hydrocynus*, *Lates*, and *Tetraodon*. Among semi-aquatic mammals, *Libycosaurus* is particularly abundant at the site, represented by young adults (three males and five females), one perinatal individual and one older juvenile. *Hexaprotodon*, including one juvenile individual, is also present but rarer. All four semi-aquatic reptile taxa are represented, including scarce remains of *Euthecodon* and Gavialoidea. Trionychidae from TM90 are large and robust, indicating old individuals. Although not analysed in this study, TM90 also preserves an exceptional diversity of waterbirds, with at least six taxa restricted to wetland habitats: *Mycteria/Ciconia* (storks), *Ephippiorhynchus/Leptoptilos* (saddle-billed and marabou storks), *Anhinga* (darters), *Plectropterus* (spur-winged geese), *Ardea* (herons), and *Heliopais* (African finfoot) (Louchart et al. 2005).
**Paleohabitat reconstruction.** The TM90 assemblage points to a calm, shallow aquatic environment with fluctuating oxygenation levels. This is reflected in the co-occurrence of oxygen-demanding taxa such as *Alestinae*, *Hydrocynus*, *Tetraodon*, and bottom-feeder catfish, alongside hypoxia-tolerant taxa like *Clariidae* and *Polypterus*, which dominate the assemblage. The presence of *Gymnarchus* further suggests the development of aquatic vegetation. Exceptional preservation, including a nearly complete *Polypterus faraou* skeleton found in anatomical connection and lying on its back (Otero et al. 2006), also supports the interpretation of a low-energy, possibly anoxic setting. Additionally, the dominance of females, young males, and juvenile *Libycosaurus* may indicate a nursery area, reinforcing the image of a close, calm and protected habitat. The abundance of *Libycosaurus* compared to *Hexaprotodon* suggests gently sloping shores and shallow aquatic settings (habitat preference hypothesis based on postcranial functional anatomy in Scribano et al., submitted).

Altogether, TM90 likely represents a swampy environment with sometimes a low oxygen level but occasionally connected to open waters, for instance, during the rainy season and flooding events.

### 3.2.2 TM242

**Description.** Aquatic and semi-aquatic taxa represent 44% of the total number of specimens of the TM242 fossil assemblage (Fig. 4). The TM242 assemblage is the smallest sample and shows the lowest diversity, with 13 identified taxa. Semi-aquatic mammals, *Libycosaurus* and *Hexaprotodon*, dominate in terms of specimen count (Fig. 6). However, the MNI presents a different pattern, with more individuals of large Claroteidae, *Synodontis*, *Alestinae*, and *Lates* (both large and small individuals), followed by *Hexaprotodon*, *Hydrocynus*, and *Semlikiichthys* (Fig. 6). *Libycosaurus* is represented only by large, mature males, while *Gymnarchus* remains correspond to large to very large individuals. *Clariidae*, *Polypterus*, *Tetraodon*, and longirostrine crocodilians are absent from this sample.

**Paleohabitat reconstruction.** The assemblage at TM242 suggests a well-oxygenated water body, likely a river or shallow lake with moderate flow. The abundance of catfish (Bagridae, Claroteidae, and *Synodontis*), *Alestinae* including *Hydrocynus*, and *Lates* further supports this idea of a flowing, oxygen-rich large water body. The presence of *Gymnarchus* and small durophagous *Alestinae* points to aquatic vegetation along the banks, and that could have supported molluscs, despite the absence of preserved evidence at TM. The dentition of these *Alestinae*, although consistent with durophagy, reflects an omnivorous diet that may have included hard-shelled prey such as gastropods and bivalves (Bailey, 1994). The relative abundance of *Hexaprotodon* compared to *Libycosaurus* (restricted to large males) suggests a more open environment, possibly with steeper banks or faster-flowing channels, offering a less sheltered habitat than at TM90.

In summary, TM242 likely represents a large, well-oxygenated freshwater habitat, possibly a flowing river or shallow lake, possibly with adjacent aquatic vegetation.

### 3.2.3 TM252

**Description.** Aquatic and semi-aquatic taxa represent 99% of the total number of specimens of the TM252 fossil assemblage (Fig. 4). The TM252 aquatic vertebrate assemblage comprises 16 taxa, with a strong dominance of *Alestinae* teeth, including *Hydrocynus* (Fig. 6). In terms of MNI, *Semlikiichthys*, *Lates* (all sizes), and Claroteidae are also well represented (Fig. 6). Various-sized *Tetraodon* are present as well. Notably, TM252, along with TM337, is the only site in Toros-Menalla that attests to the presence of the *Mormyridae Hyperopisus*. The remains at this site are highly fragmentary, consisting mainly of numerous bone splinters. However, TM252 preserves a significant number of smaller elements, including *Alestinae* teeth and many small, unidentified *Acanthomorpha*. Large semi-aquatic mammals are rare at TM252, with *Libycosaurus* represented by one male and one juvenile, while *Trionychidae* are absent.

**Paleohabitat reconstruction.** TM252, located approximately 600 meters from TM242, presents a rich assemblage with some distinct structural differences (the lowest similarity index, 58%, among the analysed sites). The presence of taxa indicative of well-oxygenated, open water, such as large individuals of *Hydrocynus*, *Lates*, and Claroteidae, is still apparent, as in TM242, but the overall ecological signal is different. The greater abundance of small *Acanthomorpha* and *Alestinae* suggests a
nutrient-rich environment. These latter, with molariform teeth, probably incorporated shelly molluscs
into their diet, but these are not preserved for taphonomic reasons (Otero et al. 2010). The presence of
*Gymnarchus* points to abundant aquatic vegetation. The relatively low presence of large semi-aquatic
mammals could support the idea of isolation.

Thus, TM252 likely represents calm, nearshore, shallow, vegetated waters, offering sheltered
conditions for small fish.

3.2.4 TM266

**Description.** Aquatic and semi-aquatic taxa represent 49% of the total number of specimens of the TM266 fossil assemblage (Fig. 4). TM266 has yielded a high diversity of aquatic vertebrates, with 20 taxa identified. This site was extensively studied and sampled due to the discovery of hominin remains (*Sahelanthropus tchadensis*; Brunet et al. 2002). All major taxonomic groups are represented, except for Cichlidae and Mormyridae. The assemblage is dominated by *Hydrocynus*, *Tetraodon*, *Lates* (all sizes), and *Libycosaurus* in terms of specimen count, while in terms of MNI, Claroteidae, *Tetraodon*, and large *Lates* individuals are the most abundant (Fig. 6). *Libycosaurus* is represented by 19 individuals (10 males and 9 females), spanning from young to old adults. A notable feature of TM266 is the attested presence of the two longirostrine crocodilian taxa (Fig. 6). Additionally, small rostra from young *Euthecodon* specimens, absent from the other sites, were recovered. TM266 also yielded brevirostrine crocodilians, including some exceptionally large individuals with well-preserved skulls. Trionychidae are present, including a complete carapace. TM266 has also yielded well-preserved catfish skulls, including Claroteidae (*Auchenoglanis* and *Clarotes*) and *Synodontis* (Otero et al. 2010). Although the skeletons are often disarticulated, their good preservation suggests short-distance transport. A larger mesh size was used at TM266 compared to the 1 mm mesh employed at other sites, which may explain why the diversity and abundance of Alestinae teeth are lower at TM266 than at sites where finer mesh sizes were used.

**Paleohabitat reconstruction.** The TM266 assemblage is dominated by taxa associated with large, well-oxygenated water bodies. These include Trionychidae, large individuals of *Lates* and *Hydrocynus* (exceeding 1 m in length), as well as *Tetraodon*, which are typical of open waters. Although *Lates* appear underrepresented in the collections, field observations indicate their remains were more abundant (Otero, pers. obs.). The high proportion of bottom-feeding catfish suggests a well-oxygenated substrate, pointing to a large but relatively shallow open water body, rather than a deep, stratified, anoxic lake. Similarly, the large proportion of *Libycosaurus* compared to *Hexaprotodon* suggests gently sloping shores and shallow aquatic settings (habitat preference hypothesis based on postcranial functional anatomy in Scribano et al., submitted). Many catfish skulls (*Clarotes*, *Auchenoglanis*, *Synodontis*) are exceptionally well-preserved but often disarticulated, indicating short-distance transport.

Unlike TM90, hypoxia-tolerant taxa do not dominate TM266. While some Clariidae remains
occur across the site, many (including articulated neurocrania) were concentrated in a restricted area,
possibly representing an ephemeral post-flooding pond (Otero et al., 2010). This points to local variation
in drainage and water depth on seasonal to interannual timescales. Additional taxa indicate habitats with
weed beds and vegetated fringes (*Tetraodon*, Alestinae) (Bailey, 1994). *Gymnarchus*, which requires
strictly fresh water because of its electro-sensory system, also occurs. Although it only depends on
aquatic vegetation during reproduction, its presence nonetheless indicates permanently freshwater
conditions.

Two non-exclusive interpretations may explain the diversity observed at TM266. On the one hand, TM266 assemblage records ephemeral spatial heterogeneity, with several coexisting and connected micro-habitats. This idea is supported by the localised concentrations of Clariidae, which may reflect temporary ponds. It is also compatible with short-term environmental fluctuations (seasonal or multi-annual) if the local topography made the area sensitive to changes in water level. Therefore, TM266 could correspond to a perilacustrine floodplain.

On the other hand, vertical mixing of fossils following deflation of the upper part of the Anthracotheriid Unit may have contributed to the taxonomic diversity. The 4-meter-thick Anthracotheriid Unit at TM266 spans an estimated depositional interval of ~0.24 Ma (7.34 ± 0.12 Ma to 7.10 ± 0.14 Ma; Lebatard et al., 2010: fig. 5), although given dating uncertainties, the duration may
range from nearly instantaneous to ~0.5 Ma. Fossils were mostly collected from surface exposures (Brunet et al., 2002). However, at TM266, this exposed surface represents an erosional surface within the ~4-m-thick Anthracotheriid Unit rather than its original top. Only the lower 1.5–2 m of the unit are preserved, the upper part having been removed by wind deflation (Lebatard et al., 2010: fig. 5). This likely led to the reworking and downward incorporation of large and resistant fossils (especially those of large semi-aquatic mammals) into the underlying layers. Therefore, part of the faunal heterogeneity could result from the temporal succession of aquatic habitats, superimposed on the primary spatial heterogeneity of the depositional environment. This issue warrants further investigation. The fish assemblages, with less resistant remains, may not have been, or to a lesser extent, affected by this vertical mixing.

### 3.2.5 TM337

**Description.** Aquatic and semi-aquatic taxa represent 95% of the total number of specimens of the TM337 fossil assemblage (Fig. 4). TM337 represents a small (couple of square meters) silty area nested within TM252, but initially appeared to exhibit a somewhat distinct fauna. Despite its limited area, the assemblage is highly diverse, containing 18 of the studied taxa. Many unidentified specimens belong to small taxa or individuals, such as small Acanthomorpha and Alestinae. *Lates* are particularly abundant, with all size classes represented, though small individuals (10-50 cm) dominate (Fig. 6). *Synodontis* is the most abundant taxon in MNI, followed by *Tetraodon* and *Semlikiichthys* (Fig. 6). Rare taxa such as *Heterotis*, molluscivorous Mormyridae, and small Cyprinidae are also present. Semi-aquatic mammals represent only a small proportion of the assemblage, with *Libycosaurus* and *Hexaprotodon* in equal proportions based on MNI. Claroteidae remains belong to large individuals. *Gymnarchus* and *Tetraodon* are primarily represented by small and medium-sized individuals, with only one or two larger specimens. Notably, large *Hydrocynus* individuals are absent.

**Paleohabitat reconstruction.** The assemblage at TM337 is largely dominated by small fish, including Alestinae and *Tetraodon*, which thrive in aquatic vegetation and marginal waters, suggesting an environment characterised by open water with weed beds and vegetated fringes, close to the canopy. While *Polypterus* and *Gymnarchus* can tolerate anoxic conditions, the presence of the other fish taxa indicates an oxygen-rich habitat. Other fish species, such as *Semlikiichthys*, numerous indeterminate small Acanthomorpha, and the rare *Labeo*, further support the interpretation of a relatively calm and sheltered environment that allowed for the preservation of fragile and minute skeletal elements.

Whenever nested within TM252, TM337 differs in its faunal structure and composition. Small fish, including fragile skeletal remains, are more prevalent, suggesting a calmer, more isolated and sheltered environment compared to TM252.

## 4. Discussion

The aquatic and semi-aquatic vertebrate assemblages from five Toros-Menalla sites reveal distinct freshwater habitats rather than a single homogeneous aquatic environment. Each assemblage reflects a distinct type of water body, ranging from perilacustrine floodplain to calm swampy zones, vegetated waters, sheltered marginal habitats, and open water bodies with flowing currents (Fig. 7). This environmental heterogeneity is consistent with patterns observed in modern African wetlands and perilacustrine or floodplain systems (Lemoalle, 2017, also see section 4.3). Such habitats likely attracted fauna from several kilometres away, concentrating wildlife around key resources such as food, breeding areas, refuges, and hunting grounds.

Available dating (Lebatard et al., 2010) indicates depositional durations of ~0.3 Ma at TM254 and ~0.2 Ma at TM266, both within a plausible range of <0.1 to ~0.5 Ma. These timescales suggest that the diversity observed among sites reflects primarily lateral spatial variation, from metres to tens of kilometres, rather than long-term temporal succession. In most cases, the fossil assemblages likely represent geologically instantaneous accumulations. The ~4 meters-thick Anthracotheriid Unit is relatively well preserved at the studied sites, and fossils were collected directly from surface exposures (e.g., TM90, TM242). Where deflation may have occurred (e.g., TM252, TM337), resistant skeletal elements indicative of post-depositional reworking are rare and do not significantly affect assemblage composition or structure. These observations support the interpretation that, except for TM266, where
vertical mixing is possible, each assemblage records a discrete depositional event within a specific
aquatic or semi-aquatic microhabitat.

The following sections examine taphonomic and sampling biases, explore links between aquatic faunal data, terrestrial assemblages, and geochemical records, and investigate broader ecosystem patterns and site formation processes through comparison with potential modern analogues.

**4.1 Taphonomic filters and sampling biases**

**4.1.1 Comparison with modern ichthyofauna**

The aquatic vertebrate diversity of Toros-Menalla provides a snapshot of Late Miocene Central African
ichthyofauna, contrasting with the present biodiversity of the Chad Basin. The Toros-Menalla
assemblage includes three extinct genera (Sindacharax, Bunocharax (Alestinae), and Semlikiichthys
(Acanthomorpha)) and two species exclusive to the site, Semlikiichthys darsao and Auchenoglanis soye
(Otero et al., 2010). Today, the basin's ichthyofauna comprises ~28 families and >170 species (Froese
and Pauly, 2025), with 14 families shared with Toros-Menalla and 15-18 absent from the fossil record.

This difference primarily reflects taphonomic processes that shaped fossil preservation. As described
for TM266 by Otero et al. (2010) and applicable to the other studied sites, the fossil fish assemblages
represent a residual signal of the original ichthyofauna, dominated by robust elements such as
neurocrania of medium to large acanthomorphs and catfishes, as well as large spines and vertebrae.

Fragile bones and remains smaller than 2–3 mm were lost likely due to wind deflation, transport, or
destruction before burial. This fraction, therefore, cannot be collected by sieving, explaining the absence
or underrepresentation of taxa with small or fragile skeletons, typical of fish families missing from
Toros-Menalla but present today in the Chad Basin (Otero et al., 2010; Froese and Pauly, 2025). This
pattern indicates moderately energetic aquatic conditions, sufficient to disarticulate fragile elements but
insufficient to polish fossil surfaces. In addition, diagenetic processes likely removed aragonitic
structures, such as otoliths and mollusc shells, despite evidence for conchophagous vertebrates (Otero
et al., 2010).

**4.1.2 Insights from mammalian and avian communities**

The taphonomic patterns observed in terrestrial mammal assemblages from Toros-Menalla provide an
independent framework to test our ecological inferences drawn from aquatic communities. Previous
studies by Le Fur et al. (2009, 2014) identified two main clusters of terrestrial assemblages among 30
Toros-Menalla sites: “TM266-like” assemblages (including TM266 and TM90) and “TM9-like”
assemblages (including TM242). These clusters are interpreted as a single original mammal
paleocommunity preserved under differing depositional regimes. TM266-like assemblages show higher
Libycosaurus abundance and greater small-taxon diversity, consistent with low-energy, quiet
depositional settings. In contrast, TM9-like assemblages are depleted in small taxa and enriched in
Hexaprotodon, reflecting higher-energy fluvial environments where fragile remains were likely
winnowed or destroyed (Le Fur et al., 2014).

These patterns closely match our aquatic-based interpretations. TM242 (part of the “TM9-like” group) displays low taxonomic richness and dominance of large, robust fish, indicative of well-oxygenated, possibly flowing freshwater conditions. For “TM9-like” assemblages, post-depositional deflation may have contributed to the loss of small remains and the overrepresentation of *Hexaprotodon* through downward incorporation of resistant elements. This appears at least possible for TM9, which evidently experienced important deflation (which is not the case of TM242). TM266 and TM90 (“TM266-like”), characterised by higher aquatic diversity and taxa adapted to vegetated, calm waters, support low-energy floodplain or swamp-like environments.

The exceptional diversity of waterbird remains at TM90 (Louchard et al., 2005) further supports the
presence of stable, resource-rich shallow waterbodies, such as marshes or lakeshores. This pattern
cannot be explained solely by favourable taphonomic conditions: for example, TM337, also interpreted
as sheltered, shallow and low-energy based on its fish assemblage, yields far fewer and less diverse bird
remains.
## 4.2 Comparison with existing paleoenvironmental proxy data

### 4.2.1 Isotopic support for assemblage-based paleoecosystem inferences

The ecological interpretations drawn from the aquatic and semi-aquatic vertebrate assemblages at Toros-Menalla are further supported by oxygen isotope data from TM90, TM266, and TM337 (Fig. 8, Jacques, 2007; Jacques et al., 2008; Otero et al., 2011; Lihoreau et al., 2014). Unpublished δ¹⁸O data from three crocodilian enamel phosphate samples were produced in the same analytical batches and using the same procedure as the fish samples published by Otero et al. (2011). For consistency across datasets, δ¹⁸O values originally reported in the V-PDB scale were converted to the V-SMOW scale using the *to_VSMOW()* function from the R package *isogeochem* (Bajnai and Tödter, 2023). When discussing the δ¹⁸O values of vertebrate remains from a given site, differences can reflect individual physiology and behaviour, mainly related to water-use strategies. Non-migratory fish (e.g., *Polypterus*) provide a strictly local hydrological signal, whereas reptiles and large mammals may access multiple sources overland, potentially integrating waters from several tens of kilometres away.

At TM90, *Polypterus* records the highest δ¹⁸O values among fish from all three sites, consistent with occupation of highly evaporated waters (Otero et al., 2011). This supports the interpretation of TM90 as a calm, poorly oxygenated waterbody dominated by *Polypterus* and *Clarias*. TM266 provides the largest isotopic dataset, offering a broad perspective on aquatic and semi-aquatic fauna. Among mammals, the strong overlap in δ¹⁸O between *Hexaprotodon* and *Libycosaurus* argues against distinct water-use niches (Jacques, 2007; Jacques et al., 2008; Lihoreau et al., 2014). The wide range observed in mammalian δ¹⁸O values (19.8–29.2 ‰) points to environmental heterogeneity at the landscape scale. Two main clusters emerge: one between 19.8–21.4 ‰, and another above 23.6 ‰. These may reflect access to different water bodies within the region, or possibly the vertical mixing processes discussed above (spanning tens to hundreds of thousands of years). Fish from TM266, including *Polypterus*, show significantly lower δ¹⁸O values than those from TM90, pointing to less evaporated conditions likely linked to differences in water drainage. The >3 ‰ offset in minimum δ¹⁸O values between the two sites cannot be explained by temperature alone (which would imply >10°C, an unlikely scenario), but is consistent with variable degrees of evaporation and hydrological connectivity across the local waterbodies. At TM337, crocodilian δ¹⁸O values are similar to those from TM266, but fish record higher values, suggesting more evaporated waters (Otero et al., 2011). This supports the interpretation of TM337 as a marginal aquatic setting, more strongly affected by evaporation than TM266.

### 4.2.2 Local vegetation reconstruction from phytolith assemblages

Phytolith assemblages provide complementary information on local vegetation at TM266 and TM337 (Novello, 2012). TM90, TM242, and TM252 proved sterile or nearly sterile in phytoliths, preventing further analysis (Novello, 2012). At TM266 and TM337, phytoliths indicate environments with an herbaceous cover dominated by grasses. TM337 shows one of the highest proportions of aquatic grass phytoliths among Toros-Menalla sites, closely matching modern assemblages from seasonal aquatic grasslands around Lake Chad (Novello, 2012; Novello et al., 2015). In contrast, indicators of arboreal cover are scarce (less than 15%), suggesting that these sites were dominated by wetland herbaceous vegetation rather than densely wooded habitats.

## 4.3 Reassessing analogue models for Toros-Menalla

The paleoecosystem of Toros-Menalla has occasionally been compared to the modern Okavango Delta, a system characterised by strong terrestrial–aquatic interactions (Brunet et al., 2004, 2005). Although never formally tested, this analogy continues to be invoked in recent literature on Toros-Menalla and early hominin environments (e.g., Su, 2024). Yet explicit and testable analogues are essential, as they (i) provide a framework to reconstruct landscape dynamics at organism-relevant spatial scales (from meters to tens of kilometres) and (ii) integrate sedimentary records, taphonomic processes, and faunal assemblages into coherent models of site formation.

This Okavango comparison is primarily based on the coexistence of terrestrial and aquatic ecosystems under semi-arid conditions. However, two major differences limit its relevance. First, faunal composition differs markedly: living fish genera from Toros-Menalla show 100% similarity with the
modern Chad-Chari and Niger basins, but only 37% with the Okavango, reflecting long-term biogeographic separation imposed by the African Central Shear Zone (Otero, 2010; Froese and Pauly, 2025). These patterns point to evolutionary histories linking Toros-Menalla more closely to Central and Western Africa than to Southern Africa. Second, hydrosystem structure differs fundamentally: the Okavango is an inland delta (subaerial fan system; Stanistreet & McCarthy, 1993) lacking a true lake, whereas Toros-Menalla records a peri-lacustrine setting organised around an open lake.

The Makgadikgadi Basin (Botswana) offers another analogue to explore. Situated within the Makgadikgadi–Okavango–Zambezi semi-arid depression, it hosted Pliocene to Late Quaternary megalakes up to ~66,000 km², with extensive shallow lagoons (Burrough et al., 2009; Burrough, 2022). Today, it is reduced to seasonally flooded pans forming shallow grass-covered wetlands. Although its present-day hydrology differs strongly from Toros-Menalla, its long-term geomorphic evolution provides a useful conceptual analogue. Notably, vegetated “dune-like islands” up to 1–2 km long occur within Ntwetwe Pan, creating strong fine-scale heterogeneity and complex terrestrial–aquatic interfaces. However, their Late Holocene aeolian origin (ca. 2–4.9 ka; Burrough, 2022), well after major paleolake stages, limits their direct relevance for the analogy with Toros-Menalla.

The Sudd wetland (South Sudan), covering ~57,000 km², is structured into channels, lagoons, permanent and seasonal swamps, and floodplain grasslands and woodlands, fed by the White Nile and local rainfall. Its ichthyofauna belongs to the Nile Basin and closely resembles that of the modern and Miocene Chad Basin (Froese and Pauly, 2025), and it hosts diverse Sahelian migratory birds and mammals (Green and El-Moghraby, 2009). While its fine-scale environmental heterogeneity makes it a useful analogue, the Sudd lacks a large, centrally organised lake and is instead dominated by a river-fed floodplain system.

These three hydrosystems illustrate fine-scale habitat heterogeneity, but none adequately captures the broader environmental setting of Toros-Menalla, particularly in terms of seasonal dynamics and spatial organisation. A more suitable analogue is therefore needed, both geographically and ecologically, to explain the diversity of aquatic habitats and their integration within a perilacustrine system.

### 4.3.1 The Bol Archipelago as a landscape analogue for Toros-Menalla

The present-day Bol Archipelago, located on the northeastern shores of Lake Chad, provides a relevant analogue for the Toros-Menalla sedimentary system (Fig. 9; Schuster, 2002). It consists of fixed dunes formed during the Last Glacial Maximum that are seasonally interannually flooded by the lake, generating a complex mosaic of channels, ponds, and ephemeral water bodies (Fig. 9A-C). Water depth in interdunal ponds decreases progressively from the open lake toward the shore, while more proximal areas preserve dry pond deposits marking former highstands. Seasonal lake-level fluctuations of 1–2 m alternately connect or isolate interdunal aquatic spaces, and floating vegetation rafts can locally block water circulation (Fig. 9D-E). These processes produce a dynamic diversity of aquatic ecosystems at the same spatial scale (a few tens of kilometres) as the Toros-Menalla fossil area.

Stratigraphic and sedimentological data independently support this analogy. At Toros-Menalla, the fossiliferous Anthracotheriid Unit was deposited over dune substrates (Vignaud et al., 2002; Schuster et al., 2006; Lebatard et al., 2010), consistent with the sequence observed at Bol (Novello et al., 2015). At Bol, the duration of the peri-lacustrine sandy claystone units can be estimated from the sedimentation rates provided by Novello et al. (2015). Using their mean sedimentation rate (54.5 m/Myr) and the thicknesses of individual sandy claystone layers measured directly from their stratigraphic log (Novello et al., 2015: fig. 2), these units likely formed over timescales ranging from several tens to a few hundred thousand years, up to ~300 kyr. Estimated durations for the Anthracotheriid Unit at Toros-Menalla (ca. 200–300 kyr) fall within the same order of magnitude (Lebatard et al., 2010), supporting comparable depositional dynamics. Eolian deposits at the base of the Toros-Menalla sequence represent the earliest evidence of a dune system in the Sahara during the Late Miocene (Schuster et al., 2006). The overlying Anthracotheriid Unit, therefore, likely developed on a dune substrate, forming an interdunal aquatic landscape. This interpretation is reinforced by the presence of emersion surfaces and cross-stratifications with multidirectional paleocurrents (Schuster, 2002; Vignaud et al., 2002; Schuster et al., 2006), which
are more consistent with water circulation between interdunal ponds than with a unidirectional fluvial
system feeding the lake.

The network of interdunal water bodies, differing in depth and connectivity, offers a natural explanation for the contrasting faunal assemblages documented across the TM sites. Within such a landscape, a rich and diverse aquatic fauna could have coexisted with dense populations of large herbivores, as historically recorded around Bol. Today, while this wild megafauna has largely extirped, the Bol Archipelago still sustains large herds of domestic cattle (Olivry et al. 1996). This makes it easy to envisage the diverse Toros-Menalla fauna evolving in such a dynamic landscape.

4.4 Implication for hominin environment reconstruction

Penecontemporaneous early hominin sites (e.g. the Tugen Hills, Kenya, yielding *Orrorin*; the Middle Awash and Gona areas – possibly Galili – yielding *Ardipithecus*) are consistently associated with rivers, lakes, or springs (e.g. Pickford and Senut, 2001; Su et al., 2009; Barboni et al., 2019; Kullmer et al., 2022; Levin et al., 2022). However, these hydrosystems are often treated as simplified, peripheral features relative to extensively studied terrestrial environments, rather than as fully integrated components of hominin ecosystems (e.g. Joordens et al., 2009; Cuthbert et al., 2017; Barboni et al., 2019; Boës et al., 2024; Gardin et al., 2024; Su, 2024).

Toros-Menalla invites us to rethink this narrative. By resolving the structure of aquatic habitats at a fine
spatial scale, this study reveals a highly heterogeneous landscape in which vegetated, fixed dune surfaces
were likely fragmented by diverse interdunal water bodies, grading toward the paleo-lake. At organism-
relevant scales, including those of hominins, aquatic and terrestrial environments were deeply
interconnected. In such a context, *Sahelanthropus* did not just live near the lakeshores; its ecological
landscape likely involved routine interaction with freshwater ecosystems and their resources.

This perspective aligns with a growing body of research highlighting the ecological importance of wetlands and aquatic resources in early hominin evolution, particularly regarding perennial drinking water access, shade, and diverse food opportunities (e.g. Stewart, 2010; Joordens et al., 2014; Cuthbert et al., 2017; Böes et al., 2024; Su, 2024), as also observed in many non-human primates today (Wrangham et al., 2009; Russon et al., 2014). Such interactions with aquatic ecosystems likely emerged early in hominin evolutionary history (Stewart, 2010; Russon et al., 2014).

4.5 Integrating aquatic fauna for richer paleoecological insights

Aquatic environments were key components of the Toros-Menalla landscape, providing resources and shelter for the terrestrial fauna. Rather than forming a uniform lakeshore margin, the fossil and geological evidence points to a complex gradient of interdigitated aquatic and terrestrial habitats intricately arranged between dune systems blending into the lake margins. In such ecosystems, a precise understanding of the structure and diversity of aquatic environments is essential. By integrating fish, semi-aquatic reptiles, and mammals' assemblages, this work captures complementary ecological information. Each group or taxon responds to distinct habitat features and at different spatial scales, allowing a more precise, multi-scalar view of freshwater ecosystem spatial diversity across the Toros-Menalla area. The representativeness of this study is strongly constrained by the limited aquatic fossil record. With crocodilians, turtles, and fish still under-represented in collections, only a handful of sites (just over five out of more than 200) presently provide assemblages suitable for analysis. Expanding systematic, grid-based, and sieving sampling is therefore crucial to obtain collections truly representative of both biodiversity and taphonomic patterns. We strongly advocate for the routine application of these methods to enhance the integration and precise characterisation of freshwater ecosystems into studies of past landscapes.

5. Conclusion

This study provides the first fine-scale reconstruction of aquatic ecosystems at Toros-Menalla based on
an integrated analysis of freshwater vertebrate assemblages, explicitly accounting for taphonomic and
sampling biases. By documenting distinct ecological signatures across five sites, it characterises part of
local heterogeneity in freshwater ecosystems and supports the proposition of a coherent modern
analogue for interpreting Toros-Menalla's landscape dynamics and site formation. This work also
defines clear priorities for future research, including expanding this approach to more TM sites,
improving sampling strategies, and testing new hypotheses on this site formation and modern analogues.

Beyond Toros-Menalla, this approach is readily transferable to other hominin-bearing sites across
intertropical Africa and complements independent paleoenvironmental proxies within multi-proxy
frameworks. It directly addresses a central challenge in hominin paleoecology: achieving the local
ecological resolution needed to understand how hominins experienced and interacted with their
environments, including the structure and role of aquatic ecosystems through time and space.

6. Acknowledgements

We are grateful to the members of the Mission Paléoanthropologique Franco-Tchadienne (MPFT) whose constant efforts over decades have made this research possible, especially Jean-Renaud Boisserie, Michel Brunet, Soizic Le Fur, and Patrick Vignaud. Among others, we warmly thank Mahamat Adoum for his work in fossil preparation and curation in the CNRD. We would also like to thank Christophe Lécuyer (LGL, Université Claude Bernard, Lyon) for allowing the geochemical analysis of previously unpublished fossil specimens, which are presented here. We thank Copernicus for Sentinel satellite images. This research was supported by the French Region Nouvelle-Aquitaine through the AH-HEM project (No. 3406720, AAP 2019), which funded the postdoctoral research fellowship of AG (2023).

7. Author contributions

A.G. and O.O. conceptualised the study based on an original idea of O.O. and G.G.; F.G. granted A.G.; F.L. and O.O. conducted dedicated fossil samplings; A.G. and C.N. managed the data. A.G., F.L., G.G., and O.O. performed the taxonomic identifications, while A.M. and M.S. contributed the geological framework and proposed the Bol Archipelago analogy; A.G. selected the methodology, performed the analyses, interpreted the data and prepared the figures; A.G. wrote the first draft of the manuscript, which was reviewed and edited by O.O.; then all authors reviewed and edited the final version and approved its submission.

8. Funding sources

This research was supported by the French Region Nouvelle-Aquitaine through the AH-HEM project (No. 3406720, AAP 2019), which funded the postdoctoral research fellowship of AG (2023).

9. Data statement

The data used in this study include specimen counts and the minimum number of individuals of semi-
aquatic and aquatic vertebrate taxa for the five studied sites in Toros-Menalla, as well as R scripts for
data processing and analysis. All datasets and scripts are available in open access on Zenodo and GitHub
via the following link: https://doi.org/10.5281/zenodo.17963310.

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Figures

<figure><img src="image_3.png" /><figcaption>**Figure 1.** Study area and geological context. A. Location of the Toros-Menalla fossiliferous area in the northern Chad Basin, with indication of major paleolake extensions. B. Map of the Toros-Menalla area showing its extension and the five study sites analysed in this work. C. Synthetic stratigraphic log of the TM266 reference section (16°15′N, 17°29′E), illustrating the three main lithological units of the Toros-Menalla sequence. The middle unit, referred to as the Anthracotherid Unit, consists of fossil-rich sandy to clayey deposits lying above an aeolian sandy unit and below a lacustrine clay-diatomite unit (modified from Moussa et al., 2021).</figcaption></figure>
<figure><img src="image_4.png" /><figcaption>**Figure 2.** Assessment and standardisation of taxonomic richness and abundance across Toros-Menalla assemblages. **A.** Rarefaction and extrapolation curves for taxonomic richness at each assemblage (aquatic and semi-aquatic vertebrates only). The x-axis represents the number of identified specimens, and the y-axis represents the estimated taxonomic richness. Solid lines indicate rarefaction based on observed data, while dashed lines represent extrapolated values. Shaded areas correspond to 95% confidence intervals. **B.** Standardisation applied to taxonomic ranks of abundance (modified from Le Fur et al., 2014).</figcaption></figure>
<figure><img src="image_5.png" /><figcaption>**Figure 3.** Hierarchical clustering of assemblages, based on the standardised taxonomic ranks of abundance, using (A) Bray–Curtis dissimilarity and (B) Euclidean distance on Hellinger-transformed data. Both methods yield similar topologies, with minor variations affecting a single assemblage (TM242). Node support values include approximately unbiased p-value (a.u.) and bootstrap probability (b.p.), the red rectangle highlights a cluster with a.u. p-value ≥ 95%.</figcaption></figure>
<figure><img src="image_6.png" /><figcaption>**Figure 4.** Relative abundance of freshwater-dwelling vertebrates and terrestrial mammals at each site. Aquatic taxa are represented in shades of blue, while terrestrial taxa are shown in shades of brown to yellow. Actinopterygians represent 97% of the TM252 assemblage, and an inset pie chart provides a detailed view of the remaining three per cent of specimens.</figcaption></figure>
<figure><img src="image_7.png" /><figcaption>**Figure 5.** Taphonomy and fish diversity at TM90. **A.** The specimen holotype of *Polypterus faraou* was found lying on its back with the ventral scales collapsed (modified from Otero et al., 2006). **B.** A delicately preserved skull of a clariid catfish. **C.** These fossils were collected in less than one square meter, by hand and illustrate the high density of clariid individuals commonly found in TM90 (e.g. there are 11 parietosupraoccipitals), while other taxa are represented by scarce fossils representing few specimens.</figcaption></figure>
<figure><img src="image_8.png" /><figcaption>**Figure 6.** Proportions of each taxonomic unit at each site. The left column shows the number of specimens per taxon, while the right column represents the taxonomic standardised ranks of abundance. Colours group taxa into broader clades to aid reading: actinopterygians in blue (dark blue for Siluriformes, light blue for Acanthomorpha, and medium blue for other taxa), crocodilians and chelonians in green, and semi-aquatic mammals in brown. At TM337, longirostrine crocodilian teeth are present but remain taxonomically unresolved between *Euthecodon* and *Gavialoidea*, so they are marked with '?'.</figcaption></figure>
<figure><img src="image_9.png" /><figcaption>**Figure 7.** Synthesis of freshwater-dwelling vertebrate assemblage analysis at Toros-Menalla. For each site, a panel summarises the main characteristics of the freshwater-dwelling vertebrate assemblages, key taphonomic indicators and the inferred type of aquatic habitat. These data are integrated to propose site-specific paleoartistic reconstructions. For TM266, no paleoartistic reconstruction is proposed due to possible vertical mixing, limiting confident landscape reconstruction.</figcaption></figure>
<figure><img src="image_10.png" /><figcaption>**Figure 8.** Stable oxygen isotope values from aquatic and semi-aquatic vertebrates in TM266, TM337 and TM90. Data from Jacques (2007), Jacques et al. (2008), Otero et al. (2011), and Lihoreau et al. (2014), and three unpublished crocodilian enamel samples.</figcaption></figure>
<figure><img src="image_11.png" /><figcaption>**Figure 9.** Satellite images of the present-day Archipelago of Bol revealing the diversity of aquatic sub-environments formed where the water of Lake Chad partly floods the Late Glacial Maximum Sand Sea of the Kanem. (A) General view of Lake Chad, forming a very large water body in drylands. Note that all the northern shore of the lake is dotted with a multitude of partially submerged barchanoïd dunes. (B) Emerged dunes (yellowish colours, sinuous shape, NW-SE long axis) compose the numerous islands of the archipelago. Note the importance of aquatic vegetation (greenish colours), and the diversity of aquatic sub-environments (open lake, archipelago, flooded interdunes). (C) Details showing the importance of fixed and mobile vegetation. (D) and (E) Details illustrating the mobility of floating vegetation which either connects or isolates water-bodies, and in turn modifies the aquatic sub-environments. Note that satellite images in false colour have been selected to better highlight mobile vegetation (in red) and water (in black). (A, B and C: Sentinel-2 L2A, True color, 2025-11-28; D: Sentinel-2 L2A, False color, 2025-12-05; E: Sentinel-2 L2A, False color, 2023-02-07).</figcaption></figure>
Tables

<table><caption>**Table 1.** Taxonomic categories of freshwater-dwelling vertebrates from Toros-Menalla, used in this article, with inferred habitat preference and tolerance based on modern relatives and, where indicated in italics, paleontological data. Habitat information refers to adult individuals unless otherwise specified.</caption><thead><tr><th>Taxonomic category</th><th>Order</th><th>Family</th><th>Genus</th><th>Habitat preference and tolerance</th><th>Refs</th></tr></thead><tbody><tr><td>Alestinae</td><td>Characiformes</td><td>Alestidae</td><td>indet.<br>(Sindacharax,<br>Alestes,<br>Brycinus)</td><td>Shallow waters and nearshore aquatic vegetation, highly oxygenated waters, lakes and drainage channels</td><td>k, j</td></tr><tr><td>Hydrocynus</td><td></td><td></td><td>Hydrocynus</td><td>Highly oxygenated waters, large rivers and lakes, and riffles<br>Juveniles are found in shallow water, lakes and drainage channels</td><td>i, j, l, p</td></tr><tr><td>Labeo<br>Cichlidae</td><td>Cypriniformes<br>Acanthomorpha</td><td>Cyprinidae<br>Cichlidae<br>(Cichliformes)</td><td>Labeo<br>indet</td><td>Rivers, riffles<br>Tolerant to medium to low oxygenation</td><td>i, k</td></tr><tr><td>Lates</td><td></td><td>Latidae<br>(Perciformes)</td><td>Lates</td><td>Well-oxygenated water, large rivers and lakes<br>Adults inhabit deep water, while juveniles are found in shallow water<br>Lateral migration of juveniles as the water level falls</td><td>m, s</td></tr><tr><td>Semlikiichthys<br>Tetraodon</td><td></td><td>incertae sedis<br>Tetraodontidae</td><td>Semlikiichthys<br>Tetraodon</td><td>Well-oxygenated water, large rivers and lakes</td><td>m, e</td></tr><tr><td>Small<br>Acanthomorpha</td><td></td><td></td><td>Juvenile fish</td><td>Shallow waters and nearshore aquatic vegetation</td><td>m</td></tr><tr><td>Polypterus</td><td>Polypteriformes</td><td>Polypteridae</td><td>Polypterus</td><td>Tolerant to low oxygenation-anoxic conditions, shallow, swampy, calm waters, floodplains</td><td>b-d</td></tr><tr><td>Gymnarchus</td><td>Osteoglossiformes</td><td>Gymnarchidae</td><td>Gymnarchus</td><td>Tolerant to low oxygenation-anoxic conditions, shallow waters and nearshore aquatic vegetation, floodplains or marshy fringes, swamps, and avoids saltwater</td><td>g, j, m</td></tr><tr><td>Heterotis</td><td></td><td>Arapaimidae</td><td>Heterotis</td><td>Open water, aquatic vegetation, floodplain and swamps<br>Tolerant of hypoxic conditions</td><td>m</td></tr><tr><td>Bagridae</td><td>Siluriformes</td><td>Bagridae</td><td>indet.</td><td>Lakes, swamps, and main river channel, riffles, and bottom-feeder<br>Avoids salt water</td><td>a, g, i, o</td></tr></tbody></table>
<table><tr><td>Clariidae</td><td>Clariidae</td><td>indet.</td><td>Tolerant to low oxygenation-anoxic conditions, Shallow, swampy, calm waters, floodplains or marshy fringes, bottom-feeder</td><td>f, j, m, t</td></tr><tr><td>Claroteidae</td><td>Claroteidae</td><td>indet.</td><td>River muddy bottom, main river channel, lakes and drainage channels, riffles, bottom-feeder</td><td>g, i, k, q</td></tr><tr><td>Mochokidae</td><td>Mochokidae</td><td>indet.</td><td>Tolerant to medium to low oxygenation, backwaters, main river channel, main channel fringes, floodplains, lakes and drainage channels, riffles, and bottom-feeder</td><td>g, i, j</td></tr><tr><td>Synodontis</td><td>Synodontis</td><td></td><td>Lakes, swamps, and rivers, muddy bottom, lakes and drainage channels, riffles, bottom-feeder</td><td>g, i, k, l, n</td></tr><tr><td>Tryonichidae</td><td>Testudines</td><td>Tryonichidae</td><td>Deep water in permanent lakes, rivers and estuaries</td><td>h</td></tr><tr><td>Crocodylus Euthecodon Gavialoidea</td><td>Crocodylia</td><td>Crocodylidae Gavialoidea</td><td>Tolerant to saline waters</td><td></td></tr><tr><td>Libycosaurus</td><td>Artiodactyla</td><td>Anthracotheriidae</td><td>700-1500kg, strongly aquatic, unable to climb steep banks, probably capable of paddle swimming and likely preferred shallow waters</td><td>r, v-w, x, y</td></tr><tr><td>Hexaprotodon</td><td>Hippopotamidae</td><td>Hexaprotodon</td><td>1500-2500 kg, strongly aquatic, capable of climbing steep banks thanks to a greater forelimb musculature, and moving in deeper, more dynamic waters such as channels and meanders</td><td>r, u-v, w, y</td></tr></table>

**References:** a. Boulenger, 1907; b. Worthington, 1929; c. Copley, 1952; d. Roberts, 1967; e. Roberts, 1986; f. Teugels, 1986; g. Bailey, 1988; h. Branch, 1988; i. Welcomme and Mérona, 1988; j. Regier et al., 1989; k. Eccles, 1992; l. Skelton, 1993; m. Bailey, 1994; n. Witte and Winter, 1995; o. Olaosebikan and Raji, 1998; p. Skelton, 2001; q. De Vos, 2001; r. Jacques, 2007; s. Liu, 2008; t. Seegers, 2008; u. Chansa et al. 2011; v. Lihoreau et al., 2014; w. Houssaye et al., 2021; x. Orliac et al., 2023, y. Scribano et al. submitted.
<table><caption>**Table 2.** Summary of the number of specimens and species, and sample coverage for each assemblage (aquatic vertebrates only). f1–f5: number of rare taxa represented by only 1 (f1) to 5 (f5) specimens in the assemblage.</caption><thead><tr><th>Assemblage</th><th>Number of specimens</th><th>Number of identified taxa</th><th>Sample coverage</th><th>f1</th><th>f2</th><th>f3</th><th>f4</th><th>f5</th></tr></thead><tbody><tr><td>TM90</td><td>694</td><td>20</td><td>0.997</td><td>2</td><td>0</td><td>1</td><td>0</td><td>2</td></tr><tr><td>TM242</td><td>177</td><td>13</td><td>0.983</td><td>3</td><td>0</td><td>3</td><td>2</td><td>0</td></tr><tr><td>TM252</td><td>2178</td><td>16</td><td>0.999</td><td>2</td><td>1</td><td>1</td><td>1</td><td>2</td></tr><tr><td>TM266</td><td>1071</td><td>20</td><td>1.000</td><td>1</td><td>0</td><td>1</td><td>0</td><td>1</td></tr><tr><td>TM337</td><td>978</td><td>18</td><td>0.998</td><td>2</td><td>1</td><td>0</td><td>0</td><td>0</td></tr></tbody></table>