Diversity, distribution and conservation of crocodiles (Order: Crocodylia) in Guinea-Bissau, West Africa

Diversity, distribution and conservation of crocodiles (Order: Crocodylia) in Guinea-Bissau, West Africa | Research Square window.SnipcartSettings = { analytics: { enabled: false } }; (function() { var accessVector = localStorage.getItem('access_vector') || ''; window.dataLayer = window.dataLayer || []; if (accessVector) { window.dataLayer.push({ user: { profile: { profileInfo: { snid: accessVector } } } }); } })(); (function(w,d,s,l,i){w[l]=w[l]||[];w[l].push({'gtm.start':new Date().getTime(),event:'gtm.js'});var f=d.getElementsByTagName(s)[0],j=d.createElement(s),dl=l!='dataLayer'?'&l='+l:'';j.async=true;j.src='https://www.googletagmanager.com/gtm.js?id='+i+dl;f.parentNode.insertBefore(j,f);})(window,document,'script','dataLayer','GTM-K279D39R'); Browse Preprints In Review Journals COVID-19 Preprints AJE Video Bytes Research Tools Research Promotion AJE Professional Editing AJE Rubriq About Preprint Platform In Review Editorial Policies Our Team Advisory Board Help Center Sign In Submit a Preprint Cite Share Download PDF Article Diversity, distribution and conservation of crocodiles (Order: Crocodylia) in Guinea-Bissau, West Africa Cristian Pizzigalli, Aissa Regalla, Ana Filipa Palmeirim, Luís Palma, and 5 more This is a preprint; it has not been peer reviewed by a journal. https://doi.org/ 10.21203/rs.3.rs-6183800/v1 This work is licensed under a CC BY 4.0 License Status: Published Journal Publication published 09 Jul, 2025 Read the published version in Scientific Reports → Version 1 posted 10 You are reading this latest preprint version Abstract Challenges in freshwater organism conservation in West Africa are worsened by significant knowledge gaps, even for charismatic species like crocodiles. This study addresses these gaps by assessing crocodile diversity, distribution, and conservation threats in Guinea-Bissau, where existing data is outdated. We used visual surveys, inquiries, molecular barcoding, camera trapping, and bibliographic reviews to investigate crocodile populations. Notably, we found evidence suggesting the Nile crocodile ( Crocodylus niloticus ), previously thought extinct in West Africa since about 200 years, may persist in the Cacheu region (Guinea-Bissau). We also confirmed the presence of the West African crocodile ( Crocodylus suchus ) in major river basins and coastal lagoons, including the Bijagós Archipelago, and the West African dwarf crocodile ( Osteolaemus cf tetraspis ) in the southern mainland and the Bijagós Archipelago. Habitat loss and deliberate killings were identified as major threats. Standardized surveys and genetic sampling are essential to assess population size, connectivity, and genetic diversity, informing evolutionary studies and conservation planning. Conservation efforts should prioritize habitat protection through community-managed reserves and restoration initiatives. Additionally, engaging local communities to raise awareness and develop conflict mitigation strategies is crucial, particularly in areas with human-crocodile interactions. Biological sciences/Ecology/Biodiversity Biological sciences/Evolution/Taxonomy Biological sciences/Zoology/Herpetology Earth and environmental sciences/Ecology/Biodiversity Earth and environmental sciences/Ecology/Biogeography Earth and environmental sciences/Ecology/Conservation Earth and environmental sciences/Ecology/Freshwater ecology West Africa non-invasive genetic habitat degradation human-wildlife conflict freshwater biodiversity Crocodylus niloticus Figures Figure 1 Figure 2 Figure 3 Introduction Freshwater organisms are among the most threatened biodiversity on the planet 1 , with major threats including pollution, dam construction, water extraction, land use change, agriculture, invasive species and disease 2 . Of these threats, agriculture and logging are the ones mostly affecting freshwater tetrapods through habitat degradation and loss 2 . This conservation crisis is exacerbated by the lack of knowledge on diversity and distribution of African wildlife, leading to a silent biodiversity decline 3 . West Africa is recognised as a global biodiversity hotspot 4–7 . However, its biodiversity is still deeply understudied when compared to other areas of the planet, with most of the published information focused on the southern countries of the region and skewed towards few taxonomic groups (i.e. mammals, birds and amphibians) 3,8 . Gaps on the diversity and distribution of organisms (Linnean and Wallacean shortfall), have deep impact in the understanding of biodiversity patterns and evolution, affecting also the efficient implementation of conservation policies 9 , even for large and charismatic species as crocodiles. Crocodilians are among the most charismatic aquatic tetrapods, playing a crucial role in their ecosystems as ecosystem engineers, apex predators and bioindicators 10–15 , being also culturally important for traditional medicine and spiritual beliefs 16 . African crocodilians are primarily found in freshwater rivers, lakes, and marshes, although some species can tolerate brackish or even saltwater. In the last 15 years, the description of the genus Mecistops, the resurrection of the West African crocodile ( Crocodylus suchus, Geoffroy Saint-Hilaire, 1807), and of the Central African slender-snouted crocodile ( Mecistops leptorhynchus, Bennett 1835) 17–19 , demonstrated that much remains to be discovered about the diversity, ecology and distribution of African crocodiles. To date, three crocodile species are known to occur in the region: 1) Crocodylus suchus is the only species of the genus Crocodylus recognised to be present in West Africa 17,20–22 . Crocodylus suchus can grow up to four metres, but most individuals are between 2 and 3.3 metres long. The smaller size and non-aggressive behaviour towards humans seem to be the only phenotypic features distinguishing this species from the larger and more aggressive Crocodylus niloticus (Laurenti, 1768) , which grows on average to more than 5 metres long 17 . Crocodylus suchus current global distribution ranges from Mauritania to the Central African Republic, and as far east as Uganda. Although more than 10 years have now passed since its resurrection as a species, the IUCN Red List assessment for C. suchus is still pending, as well as its validation as a full species and its assessment by the Convention of International Trade of Endangered Species (CITES) legislation 23 . Like other crocodilians in West Africa, this species is likely threatened by increasing anthropisation and overexploitation of natural resources, and it is traded for meat and skin in Sub-Saharan Africa 24 . 2) Mecistops cataphractus (Cuvier, 1825). The genus Mecistops was until recently considered to be monospecific, but it now comprises two species: M. cataphractus and M. leptorhynchus 18,19 . Although the historical distribution of M. cataphractus likely ranged from The Gambia to the Cameroon volcanic line 18 , the species may now be restricted to the Republic of Guinea, Ivory Coast, and Ghana, with a population persisting in the Gambia River 19 . The species is considered as Critically Endangered by the IUCN Red List, and its last assessment predates the formal description of M. leptorhynchus, therefore the Red List still considers the two Mecistops species as one 25 . The taxonomy of M. cataphractus also needs to be updated in CITES (listed as Crocodylus cataphractus in Appendix I 23 S). Current threats to the species include small-scale subsistence fisheries, which contributes to reduced availability of prey and incidental mortality in fishing nets, and habitat degradation due to the land conversion from forest to commodity plantations or settlements 19 25 . 3) The most western lineage of the genus Osteolaemus , which has a distinct evolutionary history and geographic distribution from the two congeneric recognised species, Osteolaemus tetraspis Cope, 1861 and Osteolaemus osborni (Schmidt, 1919) 26 . However, since the validity of this candidate new species had not been tested yet, and an updated taxonomic revision of the genus is still pending, we will refer to it as Osteolaemus cf tetraspis . The distribution of the O. cf tetraspis lineage has been considered to extend from The Gambia to at least Ghana 26–28 . The only IUCN Red List assessment of the genus Osteolaemus dates back to 1996 and considers the genus to be monospecific and listed as Vulnerable 29 . However, among the three lineages of the genus, O. cf tetraspis is likely to be the most threatened and with a higher risk of extinction 30 . Osteolaemus cf tetraspis is considered a valuable commodity along its distribution, and its non-aggressive nature and small size make it the most heavily hunted crocodile in West and Central Africa 15,31,32 . The CITES also recognises the genus to be monospecific ( O. tetraspis ), with all populations listed in Appendix I 23 . Hunting and human-driven habitat transformation are likely the major threats to the persistence of this taxon 30,31 . Although crocodiles are charismatic and economically valuable keystone species, the information available on their diversity, distribution and threats in Guinea-Bissau is mostly outdated and incomplete. Recent studies confirm that Crocodylus suchus is widespread across the country, while O. cf tetraspis is mostly found in the south, with some scattered populations in the Cacheu region. Both species were also present in the Bijagós Archipelago, at least until 2012 27,33 . The presence of M. cataphractus in the country has long been debated and it has been suggested that it could inhabit the coastal lagoons of Guinea-Bissau and the major watercourses in the bordering regions with Senegal and the Republic of Guinea 27 . Additionally, two large (>3.5 metres total length) crocodiles appear to be responsible for the killing of three people in the Cacheu region in 2015 34 . Crocodile attacks on humans are not new to Guinea-Bissau, although previous records were limited to the Bijagós Archipelago 33,35 . A body size greater than 3.5 metres and aggressive behaviour are not expected in C. suchus (Geoffroy Saint-Hilaire, 1807) 17 , raising the possibility that relict populations of the Nile crocodile ( Crocodylus niloticus ) may persist in the country. Crocodylus niloticus was present in West Africa in the Senegal River until at least 1803 17 . However, the species is now known to be extinct in the region and distributed only in eastern, central and southern Africa 22,36 . This study aims to provide updated information on the diversity, distribution, and conservation of crocodiles in Guinea-Bissau, by answering the following questions: 1) How many extant species of crocodiles occur in Guinea-Bissau? 2) How are these species spatially distributed? 3) What are the major threats to the persistence of crocodiles in the country? Using a combination of visual surveys, inquiries, molecular data, opportunistic bycatch images from camera trapping, and bibliographic review of the available information, we aim to provide new insights into how crocodile diversity is distributed across the country. Finally, by classifing threats following the guidelines established by the IUCN Red List Unified Classification of Direct Threats, we also aim to gather comprehensive information on the major threats facing these species in Guinea-Bissau. Results 3.1 Species Diversity The probability of assignment (PI) of our query sequences to the NCBI dataset ranged from 96–100%, with the first five sequences selected by BLAST as more similar to our query sequences. Query cover was always 100%. BLAST results highlighted the presence of three species among our sequences: Nile crocodile ( Crocodylus niloticus ), West African crocodile ( Crocodylus suchus ), and the West African dwarf crocodile ( Osteolaemus cf tetraspis ). When blasting our query sequences of C. suchus , among the 10 sequences selected by BLAST as the most similar to our query sequence, we had matching sequences labelled as C. niloticus , although they had already been identified as belonging to C. suchus in previous studies 17 , 37 . All species included in our analyses formed highly supported (> 99% pp) monophyletic lineages, except for the split between the Osteolaemus species complex and the cluster containing the genera Crocodylus and Mecistops (93% pp) (Fig. 1 ). The overall topology of our phylogenetic tree resembles the topology of the tree constructed by previous studies 17 . The results of our phylogenetic analyses clearly cluster two of our sequences with published sequences of C. niloticus from eastern and southern Africa, 44 sequences clustering with published sequences of C. suchus , and three sequences clustering with published sequences of O. cf tetraspis corresponding to the new, undescribed species. Of the 44 sequences clustering with C. suchus one (20795) from a sample collected in the eastern sector of the Corubal River considerably diverged within the species cluster with high support (100% pp) During our field surveys we found no evidence of M. cataphractus . However, local hunters and fishermen repeatedly pointed out the presence of another “type” of crocodile, which was meticulously described as having the appearance of C. suchus , but with a brownish colouration, and a longer and thinner head. 3.2. Distribution We found molecular and phenotypic (aggressive behaviour towards humans and large size) evidence for the presence of C. niloticus at three sites in the western extension of Cacheu River (Fig. 2 ). One of the Cacheu River observations of C. niloticus was confirmed by the successful molecular barcoding of the two individuals killed in the 2015 incident. Other two sites were found in the western Cacheu River based on recorded non-fatal crocodile attacks of unusual large crocodiles. The most recent non-fatal crocodile attack we recorded in the region occurred on the 27th of January 2025 in the western Cacheu River, where a fisherman was bitten on the right leg while exiting the water. We recorded C. suchus at 19 sites widely distributed across the country, mostly in the major rivers and tributaries and in fresh and brackish water lagoons. At 14 of these sites, we directly observed the species or found evidence of its presence (burrows, faeces and tracks), eight of which were confirmed by molecular identification. Two sites were found based on information from local people, and two were known from previous studies. The presence of juveniles and sub adults highlighted potentially reproducing populations in the western and eastern parts of the Cacheu River, the Geba River, the city of Bissau, the Bedasse and Cufada Lagoons, the Grande de Buba River, the Cumbidjã R. tributary, the Cacine River, and the Bijagós Islands. We recorded O. cf tetraspis at 15 sites distributed throughout southern Guinea-Bissau (Fig. 2 ). This species was found exclusively in small permanent or temporary rivers and pools surrounded by riparian forest, or in disturbed areas close to these sites (i.e. rice fields). We confirmed the presence of the species by direct observation of individuals in three sites, camera-traps records in eight sites, barcoding faecal samples in one site, and by bibliographical search in three sites. 3.3 Conservation We identified 13 types of threats potentially affecting crocodile populations and their habitats in 16 sites (Table 1 ). Crocodylus suchus was the species affected by more threats (12), followed by O. cf tetraspis (9) and C. niloticus (5). Drought and persecution/control were the most recorded threats, followed by pollution from garbage, and solid waste and soap. However, most of the threats recorded (10) have as consequence habitat loss and/or degradation. Of the threats involving direct killing of crocodiles, all the records were classified as pas, the six related to persecution/control were classified as likely to repeat, while the four related to war, and military exercises as unlikely to repeat. Table 1 Conservation threats identified in this study for crocodiles in Guinea-Bissau. The table includes threat code, definition, species affected, number and percentage of sites where the threat has been observed (total number of sites = 19). Letters in the Species column stand for: “n” C. niloticus , “s” C. suchus , “t” Osteolaemus cf tetraspis . Coding and description are based on the IUCN Red List classification scheme. Code Threats Species N of sites (%) 1.1 Housing & urban areas n, s, t 3 (15.7) 1.2 Commercial & industrial areas n, s, t 3 (15.7) 2.1.1 Shifting agriculture n, s, t 4 (21) 2.3.1 Nomadic grazing s, t 1 (5) 2.3.2 Small-holder grazing, ranching or farming s, t 3 (15.7) 3.2 Mining & quarrying s 1 (5) 5.4.3 Incidental or accidental mortality (bycatch - subsistence/small scale) s, t 3 (15.7) 5.4.5 Persecution/control n, s 6 (31.5) 6.2 War, civil unrest & military exercises s, t 4 (21) 9.1.1 Sewage s 2 (10.5) 9.1.3 Type Unknown/Unrecorded (Detergents) s 5 (26.3) 9.4 Garbage & solid waste s, t 6 (31.5) 11.2 Droughts t 7 (36.8) The two confirmed observations of C. niloticus come from two individuals killed by local authorities in 2015 because they were suspected of having eaten three people during the rainy season. Another possible C. niloticus (without molecular confirmation) was killed a few days later for the same reason at a second site in the Cacheu River. No retaliation events had followed the last human-crocodile incident that occurred on the 27th of January 2025 in the western Cacheu River. The four observations related to war, and military exercises come from the online resources. Specifically, they are three records of adults and sub-adults of either C. niloticus or C. suchus killed by the Portuguese military for bushmeat or during military operations between the years 1967 and 1974, and one O. cf tetraspis also captured by the Portuguese military around 1973–1974, all during the colonial period 34 . Inquiry data indicated that although crocodiles are occasionally eaten, they are not actively hunted for meat consumption, but their body parts are used in the production of goods (e.g., bags), traditional medicine and fetish rituals. One observation of C. suchus and one of O. cf tetraspis were from individuals which accidentally died in fishing nets in the Cacheu River and in Belí (respectively). Domestic garbage (e.g., single-use water plastic bags) is found throughout the country, but it is particularly prevalent in urban and suburban areas. In these areas, streams, drainage channels and rice fields are filled with plastic and other degradable and non-degradable waste, from animal carcasses to discarded appliances. Pollution from soap was mainly observed in urban areas where people gather around large water bodies (e.g., in Saltinho, in the Corubal River or the mangrove forest in Bissau) to wash clothes, cars and themselves. Pollution from sewage was just recorded in Bissau. We recorded evidence of land conversion, habitat degradation, and overexploitation of natural resources in the form of urban expansion, quarry mining activities near major riverbanks, shifting (slash-and-burn) agriculture, and nomadic and non-nomadic grazing. Quarry mining, and slash-and-burn agriculture were mainly recorded along the Corubal River, while nomadic and non-nomadic grazing was mostly recorded around freshwater lagoons ( wendus ). The intensifying land conversion recorded is particularly due to the increasing permanent habitat change from rainfed shifting agriculture to cashew orchards, as for instance along the Balana River. Climate change was only identified as a potential threat to O. cf tetraspis , as most of the remnant river pools where the species has been observed may disappear in the future if the extent of the dry season increases 38 . Discussion Our study gathers evidence of the presence of three crocodile species in Guinea-Bissau, distributed both on the mainland and in the Bijagós Archipelago. We have also highlighted the major threats to each species based on the IUCN Red List classification scheme. These threats are related to habitat loss, degradation, and direct killing of crocodiles. 4.1. Species Diversity and distribution The molecular barcoding of samples collected from two crocodiles killed by local authorities in the region of Cacheu during a culling operation in 2015, provide strong evidence the presence of C. niloticus in West Africa after the last confirmed observation 222 years ago 17 . These two crocodiles of 3.5 and 5 metres (full body length) were believed to be responsible for repeated attacks on pirogues and people during the 2015 rainy season, resulting in three fatalities and multiple injuries 34 . During our field expeditions surveys, we were also informed of the presence of large individuals (> 5 metres) on the island of Imbone, in the Bijagós Archipelago (Miguel Lecoq personal observation). Human-crocodile conflicts were common in the Bijagós Archipelago in the past, often resulting in fatal encounters 35 . The attacks on humans and the large body size also suggest the presence of C. niloticus on the islands. This species was last confirmed in West Africa in 1803 in the Senegal River 17 . Until now, C. niloticus was thought extinct in the region, with C. suchus considered the sole species of the genus Crocodylus 17 , 20 – 22 . Due to the lack of an accepted dichotomous key to distinguish C. niloticus from C. suchus morphologically, attacks in the Cacheu region (and the few other attacks by crocodiles of the genus Crocodylus in West Africa) were attributed to C. suchus ( https://crocattack.org/database/ ). However, our mitochondrial DNA analysis indicates that C. niloticus is likely responsible for the reported attacks on humans in the Cacheu region. To date, no comprehensive public study has compared the phenotypic traits of these two species, making it urgent to investigate potential morphological and behavioural differences. Establishing clear dichotomous characters would improve field identification and aid conservation efforts. Although our morphological, behavioral, and genetic evidence strongly supports the presence of C. niloticus in the area, our analysis is based on a fragment of mtDNA. We cannot rule out the possibility that we are detecting C. niloticus mitochondrial introgression in C. suchus , which, if confirmed, would represent the first documented case of hybridization between the two species in the wild. Therefore, future studies using nuclear molecular markers are urgently needed to confirm the presence of C. niloticus populations in Guinea-Bissau and potentially in neighbouring countries such as the Republic of Guinea, where attacks have also been recorded ( https://crocattack.org/database/ ). These areas should be promptly protected to ensure safe coexistence between human and crocodile populations. Our results confirm the presence of Osteolaemus tetraspis sensu lato in Guinea-Bissau, both on the mainland and in the Bijagós Archipelago. Our molecular identification analyses place the barcoded samples within the same clade as the undescribed lineage Osteolaemus. cf tetraspis from West Africa. This clade has already been shown to be genetically divergent from the other two species of Osteolaemus ( O. tetraspis sensu stricto and O. osborni ) 26 . Osteolaemus. cf tetraspis was (and still is) locally widely confused with the neotropical species of caimans and is commonly referred to by the non-scientific community as " jacaré " (caiman in Brazilian Portuguese) 34 . Caimans (Caimaninae; Brochu, 1999) are small to medium-sized crocodilian reptiles of the family Alligatoridae Gray 1844, native to Central and South America. These species belong to the genera Caiman , Melanosuchus , and Paleosuchus , none of which have their natural distribution in Africa; therefore, no caiman ( jacaré ) species occur naturally in Guinea-Bissau. Our observations of O. cf tetraspis are restricted to southern Guinea-Bissau and the Bijagós Archipelago. Based on the available literature 27 , the distribution of O. cf tetraspis should extend to northern Guinea-Bissau, south of Senegal and The Gambia. However, there are no recent observations of the species in southern Senegal (Casamance region), while the species was thought to be extinct in The Gambia prior to 2010 39 , when breeding populations were discovered 27 . The lack of updated observations and the increasing anthropization and land cover changes that have affected West Africa in recent decades 40 – 42 may have restricted the current global distribution of O. cf tetraspis to southern Guinea-Bissau and likely the Republic of Guinea, with possible isolated populations in The Gambia. There is an urgent need to survey the western limit of this species distribution and to assess whether O. cf tetraspis still persists in southern Senegal and northern Guinea-Bissau, and to assess the status of the remaining populations. During our field surveys, we found no direct evidence of the presence of Mecistops cataphractus . However, local hunters and fishermen consistently described sightings of a crocodile resembling C. suchus but with a brownish coloration and a longer, thinner head. These repeated accounts, along with numerous observations of unusually shaped crocodiles—especially in the south—raise intriguing questions about the possible presence of M. cataphractus or unrecognized morphological variations. Notably, the presence of this species in the region was previously highlighted 27 , further supporting the need for targeted investigations to clarify M. cataphractus presence in Guinea-Bissau. 4.2. Conservation threats Most of the threats recorded during our expeditions were led to habitat loss and/or degradation. However, the most frequently observed were droughts and direct crocodile persecution. Although crocodiles are fully protected by CITES and Guinea-Bissau wildlife law 23 , crocodile body parts remain a valuable commodity in Guinea-Bissau. Although we do not have evidence that crocodile hunting still occurs in Guinea-Bissau few hunters actively hunt them using non-automatic firearms, spears or land traps (i.e. snares) until recently 35 . Although of uknown origin, O. cf tetraspis , body parts were the most abundant crocodile items at the Bandim market in Bissau, the capital city, even surpassing those of C. suchus (CP personal observation). Due to its small size and tame behaviour, O. cf tetraspis is highly traded throughout its distribution 31 , 32 , 43 . Overhunting can lead to extinction, and disrupt population dynamics and activity patterns 44 , 45 , while unregulated bushmeat trade and consumption can increase the risk of zoonotic diseases 46 , 47 . However, little is still known on the extent of crocodile trade in Guinea-Bissau, nor on the socio-economic drivers behind the trade in crocodile body parts. Additionally, the lack of information on population size, distribution, and trends—both current and historical—combined with the uncertainty surrounding the scale of the trade, poses a serious threat to the species' persistence in the country. Urgent studies are needed to fill these knowledge gaps, strengthen conservation efforts, and prevent the silent disappearance of this still-undescribed species from Guinea-Bissau. The direct killing of crocodiles in Guinea-Bissau has mostly been driven by persecution due to human-crocodile conflict and, historically, by warfare. Crocodile hunting in Guinea-Bissau was intense during the colonial period, including with the use of automatic machine guns and grenades, and was often carried out by the Portuguese military, who had easy access to firearms 34 . Human-wildlife conflicts can be driven by several factors including climate change 48 and the intensification of environmental stressors, such as land conversion, habitat degradation, and overexploitation of natural resources 49 – 51 . The human population of Guinea-Bissau has grown by approximately 120% from 1990 to 2024 52 , intensifying environmental pressure. This has led to habitat loss due to urban expansion and commodity crop cultivation 53 , as well as habitat degradation caused by chemical pollution (e.g., domestic detergents) and slash-and-burn agriculture 54 . These changes likely exacerbate the risk of human-crocodile conflict and can result in direct disturbance and reduction of reproductive opportunities, for example through the destruction of nesting and nursery habitats (i.e. sandbanks and mangroves). The use of fire in slash-and-burn agriculture to clear natural patches of riparian forest along the Corubal River is another example. The degradation and depletion of riparian forests may lead to the rapid extinction of O. cf tetraspis 43 , which depends on the persistence of these forested environments 55 . The increase in nomadic and non-nomadic grazing, particularly around freshwater lagoons ( wendus ), also poses a threat to the persistence of crocodiles as it may lead to water shortage and pollution 56 . Finally, if the length of the dry season increases as predicted 38 suitable habitat for O. cf tetraspis might also disappear in the near future. Holistic approaches, such as agroecology, could be valuable in addressing human-wildlife conflict while implementing sustainable farming and wildlife management 57 . There is an urgent need to strengthen national and sub-national policies on habitat protection and pollution control, alongside implementing projects that promote habitat restoration and raise awareness of the importance of conserving natural ecosystems. These efforts will be crucial to mitigating the possible negative impacts of advancing climate change. Conservation management and future research Based on our findings, there is a critical need for comprehensive conservation management and research to address the lack of knowledge about crocodiles in Guinea-Bissau and the threats they are facing. As unassessed biodiversity is more likely to go extinct 58 , the taxonomic clarification of the genus Osteolaemus is urgently needed to inform and guide conservation efforts for the species in Guinea-Bissau and neighbouring countries. Future research should focus on standardized and systematic monitoring of known crocodile populations, their habitats, and trade trends, all of which are essential for more effective conservation measures. Moreover, future research should focus on the codification of dichotomous morphological characters to distinguish C. suchus and C. niloticus , as well as the use of molecular methods to confirm species identification and investigate the presence of C. niloticus in surrounding regions where human-crocodile conflicts are also occurring (e.g., Republic of Guinea). Additionally, the presence of M. cataphractus in Guinea-Bissau remains uncertain, despite reports from local hunters and fishermen describing crocodiles with distinct morphological traits. Given these accounts and previous indications 27 , further research is needed to clarify crocodile diversity in the region. Conservation actions should focus on site and habitat protection, area management, and restoration of natural processes that have been lost, especially in areas critical for the survival of O. cf tetraspis (i.e., urban areas in the northwest of the country), and to facilitate the coexistence of the human population with the potentially vulnerable populations of C. niloticus . Maintaining the protection of sacred forests has proved to be important for crocodiles 59 . Although shifts in religious beliefs in Guinea-Bissau are affecting traditional practices and the preservation of sacred forests, community-managed forests are increasingly valued in the country 60 , offering a promising solution for local crocodile conservation. Initiatives like Fédération KAFO in Djalicunda ( https://kafobissau.org/en/ ) and CHIMBO in Belí ( https://www.chimbo.org ) promote wildlife conservation through research and sustainable agroecological practices, preserving natural and cultural heritage, protecting climate-resilient ecosystems, and empowering young people to safeguard the environment. Combining community-based approaches with management strategies based on genetic research and trade regulation is essential to preserve genetic diversity and mitigate exploitation risks. Enhancing education, training, and community awareness will further reduce human-crocodile conflicts and promote crocodile conservation through biodiversity-friendly practices. Materials and Methods 2.1. Study area Guinea-Bissau, located in West Africa, is bordered by Senegal, the Republic of Guinea, and the Atlantic Ocean (Fig. 3 ). It covers 36,125 km², with a population of about 2.1 million 52 . The country features two main ecoregions: the Guinean forest-savannah mosaic and Guinean mangroves. The landscape includes scattered coastal plains, estuaries lined with mangroves, a low-elevation mosaic of dense and open forests, and savannah woodland with a peak at 310 m in the southeast. The Bijagós Archipelago comprises 88 islands, 20 of which are permanently inhabited. The monsoonal tropical climate has a dry season (November–May) and a wet season (June–October), with annual rainfall ranging from 1,500 to 3,000 mm. Vegetation includes mangroves, palm groves, wet grasslands, dry open forest, savanna woodland, dense primary and secondary forest in relict patches, and riverine galleries. The main river basins in the country are the Cacheu in the north, the Mansoa and the Geba in the centre, and the Corubal in the south (Fig. 3 ). 2.2. Data collection We visited the country during three expeditions, between 2021 and 2023. The expeditions were conducted in November/December 2021 (dry season), October/November 2022 (late rainy season, early dry season), and late April/May 2023 (dry season), for a total of 74 survey-days. During these expeditions we visited the mainland’s protected areas and most of the main rivers: Cacheu, Corubal, Geba, and Mansoa, as well as smaller tributaries and temporary rainfed lagoons (locally known as wendus ) (Fig. 3 ). Data were collected by: 1) visual surveys; 2) opportunistic sampling of genetic material (faeces and tissues) along rivers, lagoons, and other water bodies; 3) opportunistic bycatch camera-trapping data from eight sites in the south of the country, from a project aimed to survey forest elephants from 2020 to 2024 61 ; 4) opportunistic presence data from interviewing knowledgeable local people (i.e. natural guides, park rangers, hunters, shepherds, and fishermen); 5) occasional visits to bushmeat and fetish markets in Bissau where we counted the number of stalls displaying items made from crocodile body parts and tried to estimate an approximate total number of such items made from crocodile body parts; 6) bibliographic review of the available scientific and non-scientific literature. We reached survey and sampling sites by car and where possible, by canoe, accompanied by local guides, park rangers or fishermen. During boat trips, we counted individuals and collected evidence of crocodile presence (i.e. faeces, tracks and burrows). We conducted day and night visual surveys from canoes. During the canoe surveys we navigated along water bodies, with two to four people spotting live individuals or evidence of crocodile presence. Where navigation was not possible (e.g. small pools along temporary rivers under riparian forest), we reached the water bodies by car or on foot and then walked along and inside them at random. Tissue samples were collected from dead individuals killed by humans. Faecal samples were collected using sterile, disposable throat inspection wooden sticks. Tissue samples were stored in 96% ethanol until DNA extraction, while faecal samples were stored in 50ml Falcon tubes filled with sterile silica gel. The geographic location of each observation or genetic sample was recorded using a Global Positioning System (GPS) device. All methods were carried out in accordance with relevant guidelines and regulations. Fieldwork and data collection were conducted with permission from IBAP. Interviews were informal, unstructured, and anonymous, and responses were kept confidential. Informed consent was obtained from all participants involved in the study. We also recorded threats that may affect crocodiles in the country and classified them based on the Unified Classification of Direct Threats Version 3.3 provided by the IUCN Red List 62 . 2.3. Molecular identification For DNA extraction, we followed 20 . We extracted DNA from tissues samples using the DNeasy Blood & Tissue Kit (QIAGEN) and from faecal samples using the GuSCN/silica method 63 . For faecal samples we performed extraction and pre-PCR procedures at BIOPOLIS-CIBIO research centre in dedicated low-quality DNA facilities, sterilised and equipped with positive air pressure and UV lights. For DNA barcoding analyses we amplified a 421 base pair (bp) 12S mitochondrial DNA (mtDNA) fragment in 10 µl reaction volume, containing 5 µl of master mix (Multiplex PCR Kit, QIAGEN), 0.5 uM of each primer and between 1 and 2 µl of DNA for tissue and faecal samples, respectively. Primer information and PCR conditions were the same as in Table S2 of Velo-Anton et al. (2014). We performed cycle sequencing for both strands using PCR primers and the ABI PRISM BigDye Terminator kit (AB Applied Biosystems) in a MyCycler BioRad Thermal Cycler and sequenced PCR products on an ABI 3130xl Genetic Analyzer (AB Applied Biosystems). We checked and edited electropherograms by eye and aligned all sequences using GENEIOUS PRIME 2024.0.7. We then downloaded available 12S sequences of Crocodylus niloticus, C. suchus , C. porosus (Schneider, 1801), Osteolaemus osborni, O. tetraspis, O. cf tetraspis, Mecistops cataphractus, M. leptorhynchus, Gavialis gangeticus (Gmelin, 1789), Tomistoma schlegelii (Müller, 1838) from previous publications 20 , 26 , 37 , 64 – 66 . The final alignment contains a total of 142 sequences with a length of 313 bp. The first step of our species identification was performed in BLASTn ( https://blast.ncbi.nlm.nih.gov/Blast.cgi ) to compare our query sequences with the NCBI reference sequence database. Sequences were identified at the species level when the percentage of identification was higher than 96% for the first 10 matching sequences in the NCBI database. Since some available sequences from C. suchus are still named as C. niloticus in the NCBI database, we performed a Bayesian inference analysis using BEAST 2.5 67 to establish the correct phylogenetic position of our sequences from the three genera. We run three separate analyses, each for 10 7 generations with sampling at every 10 3 MCMC steps. We used the strict clock model and the Coalescent Constant Population prior. We used IQ-TREE 68 to infer the model to be assigned to the appropriate partitions. We used Tracer V1.7.2 69 to visualise the log file of each run and summarise the analytic statistics. The effective sample size was sufficient for all statistics (ESS > 200). We then used LogCombiner to combine the tree files from each run discarding a 10% burn-in. We used TreeAnnotator to produce the maximum credibility tree and annotate the 95% highest probability density ranges. Declarations Acknowledgments We would like to acknowledge the Guinea-Bissau governmental agency Instituto de Biodiversidade e Áreas Protegidas (IBAP), namely the former director Dr. Justino Biai for fieldwork and sampling permits. We are grateful to the CHIMBO NGO, Ana Rainho and her research team, the workers of the NGO KAFO (Guinea-Bissau), and to the people of Djalicunda, Farim and all the tabanca visited during our expeditions for the valuable information provided, their time, and the amazing hospitality. Acknowledgements extended to Pierre Campredon and António Araújo for facilitating crocodile samples and to Miguel Lecoq for providing extensive information on the crocodiles in the Bijagos Islands. Fieldwork was financed by the project TROPIBIO (CIBIO, Vairão, Portugal; European Union's Horizon 2020 research and innovation programme under grant agreement no. 854248). Camera trapping was co-funded by the Elephant Crisis Fund (Save the Elephants/Wildlife Conservation Network) - Projects GW_ICE-01, GW_CIB_02 and 03). CP, JCB, MLL and RG are financed by FCT - Fundação para a Ciência e Tecnologia (2020.05054.BD, CEECINST/00014/2018/CP1512/CT0001, CEECINSTLA/00020/2022 and 2022.07926. CEECIND, respectively), LP and field missions were supported by national Portuguese funds through FCT - InBIO Programático FUI 2020-2023 (UIDP/50027/2020). Author contributions CP, OR, RG, and JCB conceptualised the study, its methodology and wrote the original draft of the manuscript; CP performed the formal analyses under JCB, OR, and RG supervision; CP, LP, WAI, OR, RG and JCB were gathered data and resources needed for the developing of the applied methodology; CP, LP, WAI, RG, and JCB curated the data; CP, AFP, LP, ML, RG, and JCB acquired the financial support for the project leading to this publication. All the authors contributed to the preparation, creation and presentation of the published work. Data availability statement The datasets generated and analysed during the current study are available in the Zenodo repository at: https://zenodo.org/records/14975165?preview=1&token=eyJhbGciOiJIUzUxMiJ9.eyJpZCI6ImVkMzdmY2Y4LTI2MGQtNDgzZC1iNzc1LTM4Y2RlNmFiMTE5MCIsImRhdGEiOnt9 LCJyYW5kb20iOiJjYWJjNmZkODFmMWEwOTRjODQ4NWJkZDllZmI2MDdkOCJ9.FM70mJCXkMrMRTbTTlyCL6DlWSLb631k--QDgTInLZdxuO-L_NMhWO8Ua2T-r2jga1nocp8XSpvbgPdoxlvTBw References Albert, J. S. et al. Scientists’ warning to humanity on the freshwater biodiversity crisis. Ambio 50 , 85–94 (2021). Sayer, C. A. et al. One-quarter of freshwater fauna threatened with extinction. Nature 638 , 138–145 (2025). Farooq, H., Azevedo, J. A. R., Soares, A., Antonelli, A. & Faurby, S. Mapping Africa’s Biodiversity: More of the Same Is Just Not Good Enough. Syst. Biol. 70 , 623–633 (2021). Myers, N., Mittermeier, R. A., Mittermeier, C. G., Da Fonseca, G. A. B. & Kent, J. Biodiversity hotspots for conservation priorities. Nature 403 , 853–858 (2000). Oates, J. F., Bergl, R. A. & Linder, J. M. Africa’s Gulf of Guinea Forests: Biodiversity Patterns and Conservation Priorities. Brito, J. C. et al. Unravelling biodiversity, evolution and threats to conservation in the Sahara‐Sahel. Biol. Rev. 89 , 215–231 (2014). dos Reis-SilvaF., P., A. F. Amphibian and reptile dataset across different land-use types in Guinea-Bissau. (2024) doi:https://doi.org/10.1101/2024.11.21.624282. Luiselli, L. et al. State of knowledge of research in the Guinean forests of West Africa region. Acta Oecologica 94 , 3–11 (2019). Hortal, J. et al. Seven Shortfalls that Beset Large-Scale Knowledge of Biodiversity. Annu. Rev. Ecol. Evol. Syst. 46 , 523–549 (2015). Mazzotti, F. J. et al. Alligators and crocodiles as indicators for restoration of Everglades ecosystems. Ecol. Indic. 9 , S137–S149 (2009). Van Der Ploeg, J., Cauillan-Cureg, M., Van Weerd, M. & Persoon, G. ‘Why must we protect crocodiles?’ Explaining the value of the Philippine crocodile to rural communities. J. Integr. Environ. Sci. 8 , 287–298 (2011). Somaweera, R. et al. The ecological importance of crocodylians: towards evidence‐based justification for their conservation. Biol. Rev. 95 , 936–959 (2020). Humphries, M. S., Myburgh, J. G., Campbell, R., Buah-Kwofie, A. & Combrink, X. Organochlorine pesticide bioaccumulation in wild Nile crocodile (Crocodylus niloticus) fat tissues: Environmental influences on changing residue levels and contaminant profiles. Sci. Total Environ. 753 , 142068 (2021). Rainwater, T. R. et al. Fauna Associated with American Alligator (Alligator mississippiensis) Nests in Coastal South Carolina, USA. Animals 14 , 620 (2024). Ouré, R. B. & Sinsin, B. Does Crocodile Conservation Matter in Sacred Natural Sites of Benin (Western Africa)? West Afr. J. Appl. Ecol. 31 , (2023). Pooley, S. A Cultural Herpetology of Nile Crocodiles in Africa. Conserv. Soc. 14 , 391–405 (2016). Hekkala, E. et al. An ancient icon reveals new mysteries: Mummy DNA resurrects a cryptic species within the Nile crocodile. Mol. Ecol. 20 , 4199–4215 (2011). Shirley, M. H., Vliet, K. A., Carr, A. N. & Austin, J. D. Rigorous approaches to species delimitation have significant implications for African crocodilian systematics and conservation. Proc. R. Soc. B Biol. Sci. 281 , 20132483 (2014). Shirley, M. H., Carr, A. N., Nestler, J. H., Vliet, K. A. & Brochu, C. A. Systematic revision of the living African slender-snouted crocodiles (Mecistops gray, 1844). Zootaxa 4504 , 151–193 (2018). Velo-Antón, G., Godinho, R., Campos, J. C. & Brito, J. C. Should i stay or should i go? Dispersal and population structure in small, isolated desert populations of west african crocodiles. PLoS ONE 9 , (2014). Cunningham, S. W., Shirley, M. H. & Hekkala, E. R. Fine scale patterns of genetic partitioning in the rediscovered African crocodile, Crocodylus suchus (Saint-Hilaire 1807). PeerJ 2016 , (2016). van Asch, B. et al. Phylogeography, genetic diversity, and population structure of Nile crocodile populations at the fringes of the southern African distribution. PLoS ONE 14 , (2019). UNEP-WCMC. UNEP-WCMC Species Database: CITES-Listed Species. (2024). Luiselli, L. et al. Understanding the influence of non-wealth factors in determining bushmeat consumption: Results from four West African countries. Acta Oecologica 94 , 47–56 (2019). Shirley, M.H. Mecistops cataphractus: Shirley, M.H.: The IUCN Red List of Threatened Species 2014: e.T5660A3044332. https://doi.org/10.2305/IUCN.UK.2014-1.RLTS.T5660A3044332.en (2013). Eaton, M. J., Martin, A., Thorbjarnarson, J. & Amato, G. Species-level diversification of African dwarf crocodiles (Genus Osteolaemus): A geographic and phylogenetic perspective. Mol. Phylogenet. Evol. 50 , 496–506 (2009). Trape, J.-F., Trape, S. & Chirio, L. Lézards, Crocodiles et Tortues d’Afrique Occidentale et Du Sahara . (IRD Éditions, 2012). doi:10.4000/books.irdeditions.37699. Smolensky, N. L., Hurtado, L. A. & Fitzgerald, L. A. DNA barcoding of Cameroon samples enhances our knowledge on the distributional limits of putative species of Osteolaemus (African dwarf crocodiles). Conserv. Genet. 16 , 235–240 (2015). Ross J.P. Crocodiles. Status Survey and Conservation Action Plan. 2nd Edition. IUCN/SSC Crocodile Specialist Group. (1998). Naabeh, C. S. S., Oppong, S. K., Amoah, E., Ahmed, S. & Anokye, A. The Vulnerable West African Dwarf Crocodile (Osteolaemus Sp. Aff. Tetraspis) is Worth Conserving in Urban Ecosystems: Evidence from Ghana. Preprint at https://doi.org/10.21203/rs.3.rs-2778658/v1 (2023). Ogorode, O., Vincent-Akpu, F., Babatunde, B., Ijeomah, M. & Olaleru, F. ILLEGAL WILDLIFE TRADE AND OSTEOLAEMU STETRASPIS: A CASE STUDY OF ACTIVITIES IN BUSHMEAT MARKETS UWA AND EDUMANOM IN NIGER DELTA, NIGERIA. (2023). Olunusi, B. O. Wildlife trade dynamics: exploring bushmeat market with a view toward social and ecological justice in Ibadan Metropolis Nigeria. Front. Conserv. Sci. 5 , 1401308 (2024). Auliya, M., Wagner, P. & Böhme, W. The herpetofauna of the Bijagós archipelago, Guinea-Bissau (West Africa) and a first country-wide checklist. Graça L. Fotos à procura de... uma legenda (153): Uma vez por todas, não havia nem há ‘jacarés’ na Guiné-Bissau, mas ‘crocodilos’ (e outros répteis). Luís Graça & Camaradas da Guiné https://blogueforanadaevaotres.blogspot.com/2021/07/guine-6174-p22399-fotos-procura-de-uma.html. Benoit Limoges & Marie-Josée Robillard. Proposition d’un plan d’aménagement de la réserve de la biosphère de l’archipel des Bijagos. Volume 2. Les espèces. (1991) doi:10.13140/RG.2.2.17554.79044. IUCN. Crocodylus niloticus: Isberg, S., Combrink, X., Lippai, C. & Balaguera-Reina, S.A.: The IUCN Red List of Threatened Species 2019: e.T45433088A3010181. https://doi.org/10.2305/IUCN.UK.2019-1.RLTS.T45433088A3010181.en (2017). Schmitz, A. et al. Molecular evidence for species level divergence in African Nile Crocodiles Crocodylus niloticus (Laurenti, 1786). Comptes Rendus Palevol 2 , 703–712 (2003). Kumi, N. & Abiodun, B. J. Potential impacts of 1.5 °C and 2 °C global warming on rainfall onset, cessation and length of rainy season in West Africa. Environ. Res. Lett. 13 , 055009 (2018). Barnett, L. K., Emms, C. & Santoni, C. THE HERPETOFAUNA OF ABUKO NATURE RESERVE, THE GAMBIA. (2001). Venter, J. A., Fouché, P. S. O. & Vlok, W. Current distribution of the southern barred minnow, Opsaridium peringueyi (Pisces: Cyprinidae), in South Africa: Is there reason for concern? Afr. Zool. 45 , 244–253 (2010). Brandt, M. et al. Reduction of tree cover in West African woodlands and promotion in semi-arid farmlands. Nat. Geosci. 11 , 328–333 (2018). Herrmann, S. M., Brandt, M., Rasmussen, K. & Fensholt, R. Accelerating land cover change in West Africa over four decades as population pressure increased. Commun. Earth Environ. 1 , 53 (2020). Ayamba, A. J., Thomas, T. K., Ajebe, H. N., Juscar, N. & Venceslas, P. M. Distribution of Dwarf Crocodile (Osteolaemus Tetraspis Cope, 1861) Populations on the Outskirts of the Ebo Forest: Implications for Conservation. Am. J. Environ. Stud. 7 , 1–14 (2024). Ferreira Da Silva, M. J. et al. Disrupted dispersal and its genetic consequences: Comparing protected and threatened baboon populations (Papio papio) in West Africa. PLOS ONE 13 , e0194189 (2018). Becker, M. S. et al. Wire-snare bushmeat poaching and the large African carnivore guild: Impacts, knowledge gaps, and field-based mitigation. Biol. Conserv. 289 , 110376 (2024). Wegner, G. I. et al. Averting wildlife-borne infectious disease epidemics requires a focus on socio-ecological drivers and a redesign of the global food system. eClinicalMedicine 47 , 101386 (2022). Public health risks involved in the human consumption of reptile meat - Scientific Opinion of the Panel on Biological Hazards. EFSA J. doi:10.2903/j.efsa.2007.578. Abrahms, B. et al. Climate change as a global amplifier of human–wildlife conflict. Nat. Clim. Change 13 , 224–234 (2023). Mekonen, S. Coexistence between human and wildlife: the nature, causes and mitigations of human wildlife conflict around Bale Mountains National Park, Southeast Ethiopia. BMC Ecol. 20 , 51 (2020). Chakanyuka, T. & Utete, B. Adaptive co‐management, co‐existence or just wildlife conservation? Case study of the human and Nile crocodile ( Crocodylus niloticus ) conflicts in Ngezi Dam, Mashonaland West, Zimbabwe. Afr. J. Ecol. 60 , 759–768 (2022). Ashepet, M.-G., Dahdouh-Guebas, F., Redpath, S., Pooley, S. & Huge, J. The state and perceptions of human-crocodile interactions around Murchison falls conservation area, Uganda. Hum. Dimens. Wildl. 29 , 194–209 (2024). World Bank. Guinea-Bissau: Development news, research, data. World Development Indicators. https://data.worldbank.org/country/guinea-bissau. https://data.worldbank.org/country/guinea-bissau. Raimundo Lopes, N. D., Li, T., Qian, D., Matomela, N. & Sá, R. M. Factors influencing coastal land cover change and corresponding impact on habitat quality in the North-western Coastline of Guinea-Bissau (NC-GB). Ocean Coast. Manag. 224 , 106181 (2022). Temudo, M. P. & Santos, P. Shifting environments in Eastern Guinea-Bissau, West Africa: The length of fallows in question. NJAS Wagening. J. Life Sci. 80 , 57–64 (2017). Amoah, E., Danquah, E. & Perran Ross, J. Nesting Ecology of West African Dwarf Crocodiles in a Heavily Disturbed Landscape in Chirehin, Ghana. Int. J. Ecol. 2021 , 1–11 (2021). Campos, J. C., Martínez-Freiría, F., Sousa, F. V., Santarém, F. & Brito, J. C. Update of distribution, habitats, population size, and threat factors for the West African crocodile in Mauritania. Amphib. Reptil. 37 , 325–330 (2016). Matangi, D. Understanding Human-wildlife conflict and its impact on agroecology transition In Zimbabwe. Tech. Rep. Liu, C., Hu, Y., Taukenova, A., Tian, G. & Mu, B. Identification of Wetland Conservation Gaps in Rapidly Urbanizing Areas: A Case Study in Zhengzhou, China. Land 12 , (2023). Kpéra, G. N. et al. ‘A pond with crocodiles never dries up’: a frame analysis of human–crocodile relationships in agro-pastoral dams in Northern Benin. Int. J. Agric. Sustain. 12 , 316–333 (2014). Palmeirim, A. F., Seck, S., Palma, L. & Ladle, R. J. Shifting values and the fate of sacred forests in Guinea-Bissau: are community-managed forests the answer? Environ. Conserv. 50 , 152–155 (2023). Palma, L. et al. African Forest elephants persist in Guinea-Bissau but require an emergency conservation plan. Oryx 58 , 125–128 (2024). IUCN. Unified Classification of Direct Threats Version 3.3. (2022). Boom, R. et al. Rapid and simple method for purification of nucleic acids. J. Clin. Microbiol. 28 , 495–503 (1990). Janke, A. & Arnason, U. The complete mitochondrial genome of Alligator mississippiensis and the separation between recent archosauria (birds and crocodiles). Mol. Biol. Evol. 14 , 1266–1272 (1997). Franke, F. A. et al. Genetic differentiation of the African dwarf crocodile Osteolaemus tetraspis Cope, 1861 (Crocodylia: Crocodylidae) and consequences for European zoos. Org. Divers. Evol. 13 , 255–266 (2013). Hekkala, E. R. et al. The secrets of Sobek – A crocodile mummy mitogenome from ancient Egypt. J. Archaeol. Sci. Rep. 33 , (2020). Bouckaert, R. et al. BEAST 2.5: An advanced software platform for Bayesian evolutionary analysis. PLOS Comput. Biol. 15 , e1006650 (2019). Minh, B. Q. et al. IQ-TREE 2: New Models and Efficient Methods for Phylogenetic Inference in the Genomic Era. Mol. Biol. Evol. 37 , 1530–1534 (2020). Rambaut, A., Drummond, A. J., Xie, D., Baele, G. & Suchard, M. A. Posterior Summarization in Bayesian Phylogenetics Using Tracer 1.7. Syst. Biol. 67 , 901–904 (2018). Additional Declarations No competing interests reported. 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11:23:14","currentVersionCode":1,"declarations":"","doi":"10.21203/rs.3.rs-6183800/v1","doiUrl":"https://doi.org/10.21203/rs.3.rs-6183800/v1","draftVersion":[],"editorialEvents":[{"content":"https://doi.org/10.1038/s41598-025-08789-3","type":"published","date":"2025-07-09T15:57:45+00:00"}],"editorialNote":"","failedWorkflow":false,"files":[{"id":79549803,"identity":"36a140fc-48df-4bee-a327-6383b9e99d9a","added_by":"auto","created_at":"2025-03-31 06:27:54","extension":"png","order_by":1,"title":"Figure 1","display":"","copyAsset":false,"role":"figure","size":748617,"visible":true,"origin":"","legend":"\u003cp\u003ePlacement of study samples within the African crocodilian phylogenetic tree. Colours of the branches refer to the species found in Guinea-Bissau in this study, namely: the Nile crocodile (\u003cem\u003eC. niloticus \u003c/em\u003ein green), the West African crocodile (\u003cem\u003eC. suchus \u003c/em\u003ein yellow), and the West African dwarf crocodile (\u003cem\u003eO. cf tetraspis\u003c/em\u003e in purple). Red dots at the nodes represent highly supported nodes (\u0026gt;95% pp), coloured dots next to the branch description represent the samples collected for this study.\u003c/p\u003e","description":"","filename":"1.png","url":"https://assets-eu.researchsquare.com/files/rs-6183800/v1/5f26fae84bba4a196f51cc06.png"},{"id":79549813,"identity":"c7206c6d-b52b-48c2-8d0a-a40cd9d42741","added_by":"auto","created_at":"2025-03-31 06:27:55","extension":"png","order_by":2,"title":"Figure 2","display":"","copyAsset":false,"role":"figure","size":215720,"visible":true,"origin":"","legend":"\u003cp\u003eDistribution of crocodile data collected in Guinea-Bissau.\u003cstrong\u003e \u003c/strong\u003eSymbols with red strokes represent barcoded genetic samples.\u003c/p\u003e","description":"","filename":"2.png","url":"https://assets-eu.researchsquare.com/files/rs-6183800/v1/c83e9eba06518d6adfaa18d0.png"},{"id":79549814,"identity":"63bf4502-1891-4be4-a955-4f453761cd5a","added_by":"auto","created_at":"2025-03-31 06:27:55","extension":"png","order_by":3,"title":"Figure 3","display":"","copyAsset":false,"role":"figure","size":698807,"visible":true,"origin":"","legend":"\u003cp\u003eMap of the toponymies in the study area. Triangles indicate the major cities, whose names are adjacent to them.\u003cstrong\u003e \u003c/strong\u003eNumbers in bold indicate the protected areas: 1) Tarrafes do Rio Cacheu National Park, 2) Boe National Park, 3) Tchetche Natural Corridor, 4) Dulombi National Park, 5) Salifo-Xitole Natural Corridor, 6) Cuntabani-Quebo Natural Corridor, 7) Cantanhez National Park, 8) Lagoas de Cufada Natural Park and 9) Grupo de Ilhas de Orango National Park.\u003c/p\u003e","description":"","filename":"3.png","url":"https://assets-eu.researchsquare.com/files/rs-6183800/v1/3b8918411f5800665a6b6900.png"},{"id":86699427,"identity":"9bd968ce-973b-40c1-b17e-fc2aeae2e6ab","added_by":"auto","created_at":"2025-07-14 16:09:29","extension":"pdf","order_by":0,"title":"","display":"","copyAsset":false,"role":"manuscript-pdf","size":2498688,"visible":true,"origin":"","legend":"","description":"","filename":"manuscript.pdf","url":"https://assets-eu.researchsquare.com/files/rs-6183800/v1/5060b1ad-802d-490b-bdea-8ca3b101b08f.pdf"}],"financialInterests":"No competing interests reported.","formattedTitle":"Diversity, distribution and conservation of crocodiles (Order: Crocodylia) in Guinea-Bissau, West Africa","fulltext":[{"header":"Introduction","content":"\u003cp\u003eFreshwater organisms are among the most threatened biodiversity on the planet\u003csup\u003e1\u003c/sup\u003e, with major threats including pollution, dam construction, water extraction, land use change, agriculture, invasive species and disease\u003csup\u003e2\u003c/sup\u003e. Of these threats, agriculture and logging are the ones mostly affecting freshwater tetrapods through habitat degradation and loss\u003csup\u003e2\u003c/sup\u003e. This conservation crisis is exacerbated by the lack of knowledge on diversity and distribution of African wildlife, leading to a silent biodiversity decline\u003csup\u003e3\u003c/sup\u003e. West Africa is recognised as a global biodiversity hotspot\u003csup\u003e4–7\u003c/sup\u003e. However, its biodiversity is still deeply understudied when compared to other areas of the planet, with most of the published information focused on the southern countries of the region and skewed towards few taxonomic groups (i.e. mammals, birds and amphibians)\u003csup\u003e3,8\u003c/sup\u003e. Gaps on the diversity and distribution of organisms (Linnean and Wallacean shortfall), have deep impact in the understanding of biodiversity patterns and evolution, affecting also the efficient implementation of conservation policies\u003csup\u003e9\u003c/sup\u003e, even for large and charismatic species as crocodiles.\u0026nbsp;\u003c/p\u003e\n\u003cp\u003eCrocodilians are among the most charismatic aquatic tetrapods, playing a crucial role in their ecosystems as ecosystem engineers, apex predators and bioindicators\u003csup\u003e10–15\u003c/sup\u003e, being also culturally important for traditional medicine and spiritual beliefs\u003csup\u003e16\u003c/sup\u003e. African crocodilians are primarily found in freshwater rivers, lakes, and marshes, although some species can tolerate brackish or even saltwater. In the last 15 years, the description of the genus \u003cem\u003eMecistops,\u0026nbsp;\u003c/em\u003ethe resurrection of the West African crocodile (\u003cem\u003eCrocodylus suchus,\u0026nbsp;\u003c/em\u003eGeoffroy Saint-Hilaire, 1807), and of the Central African slender-snouted crocodile (\u003cem\u003eMecistops leptorhynchus,\u0026nbsp;\u003c/em\u003eBennett 1835)\u003csup\u003e17–19\u003c/sup\u003e, demonstrated that much remains to be discovered about the diversity, ecology and distribution of African crocodiles. To date, three crocodile species are known to occur in the region:\u003c/p\u003e\n\u003cp\u003e1) \u003cem\u003eCrocodylus suchus\u0026nbsp;\u003c/em\u003eis the only species of the genus \u003cem\u003eCrocodylus\u0026nbsp;\u003c/em\u003erecognised to be present in West Africa\u003csup\u003e17,20–22\u003c/sup\u003e. \u003cem\u003eCrocodylus suchus\u003c/em\u003e can grow up to four metres, but most individuals are between 2 and 3.3 metres long. The smaller size and non-aggressive behaviour towards humans seem to be the only phenotypic features distinguishing this species from the larger and more aggressive \u003cem\u003eCrocodylus niloticus\u0026nbsp;\u003c/em\u003e(Laurenti, 1768)\u003cem\u003e,\u003c/em\u003e which grows on average to more than 5 metres long\u003csup\u003e17\u003c/sup\u003e. \u003cem\u003eCrocodylus suchus\u003c/em\u003e current global distribution ranges from Mauritania to the Central African Republic, and as far east as Uganda. \u0026nbsp;Although more than 10 years have now passed since its resurrection as a species, the IUCN Red List assessment for \u003cem\u003eC. suchus\u0026nbsp;\u003c/em\u003eis still pending, as well as its validation as a full species and its assessment by the Convention of International Trade of Endangered Species (CITES) legislation\u003csup\u003e23\u003c/sup\u003e. Like other crocodilians in West Africa, this species is likely threatened by increasing anthropisation and overexploitation of natural resources, and it is traded for meat and skin in Sub-Saharan Africa\u003csup\u003e24\u003c/sup\u003e.\u003c/p\u003e\n\u003cp\u003e2) \u003cem\u003eMecistops cataphractus\u003c/em\u003e (Cuvier, 1825). The genus \u003cem\u003eMecistops\u003c/em\u003e was until recently considered to be monospecific, but it now comprises two species: \u003cem\u003eM. cataphractus\u0026nbsp;\u003c/em\u003eand\u003cem\u003e\u0026nbsp;M. leptorhynchus\u003c/em\u003e \u003csup\u003e18,19\u003c/sup\u003e. Although the historical distribution of \u003cem\u003eM. cataphractus\u003c/em\u003e likely ranged from The Gambia to the Cameroon volcanic line\u003csup\u003e18\u003c/sup\u003e, the species may now be restricted to the Republic of Guinea, Ivory Coast, and Ghana, with a population persisting in the Gambia River\u003csup\u003e19\u003c/sup\u003e. The species is considered as Critically Endangered by the IUCN Red List, and its last assessment predates the formal description of \u003cem\u003eM. leptorhynchus,\u0026nbsp;\u003c/em\u003etherefore the Red List still considers the two \u003cem\u003eMecistops\u003c/em\u003e species as one\u003csup\u003e25\u003c/sup\u003e. The taxonomy of \u003cem\u003eM. cataphractus\u003c/em\u003e also needs to be updated in CITES (listed as \u003cem\u003eCrocodylus cataphractus\u003c/em\u003e in Appendix I\u003csup\u003e23\u003c/sup\u003eS). Current threats to the species include small-scale subsistence fisheries, which contributes to reduced availability of prey and incidental mortality in fishing nets, and habitat degradation due to the land conversion from forest to commodity plantations or settlements\u003csup\u003e19\u003c/sup\u003e\u003csup\u003e25\u003c/sup\u003e.\u003c/p\u003e\n\u003cp\u003e3) The most western lineage of the genus \u003cem\u003eOsteolaemus\u003c/em\u003e, which has a distinct evolutionary history and geographic distribution from the two congeneric recognised species, \u003cem\u003eOsteolaemus tetraspis\u0026nbsp;\u003c/em\u003eCope, 1861 and \u003cem\u003eOsteolaemus osborni\u003c/em\u003e (Schmidt, 1919)\u003csup\u003e26\u003c/sup\u003e. However, since the validity of this candidate new species had not been tested yet, and an updated taxonomic revision of the genus is still pending, we will refer to it as \u003cem\u003eOsteolaemus cf tetraspis\u003c/em\u003e. The distribution of the \u003cem\u003eO. cf tetraspis\u003c/em\u003e lineage has been considered to extend from The Gambia to at least Ghana\u003csup\u003e26–28\u003c/sup\u003e. The only IUCN Red List assessment of the genus \u003cem\u003eOsteolaemus\u0026nbsp;\u003c/em\u003edates back to 1996 and considers the genus to be monospecific and listed as Vulnerable\u003csup\u003e29\u003c/sup\u003e. However, among the three lineages of the genus, \u003cem\u003eO. cf tetraspis\u003c/em\u003e is likely to be the most threatened and with a higher risk of extinction\u0026nbsp;\u003csup\u003e30\u003c/sup\u003e. \u003cem\u003eOsteolaemus cf tetraspis\u003c/em\u003e is considered a valuable commodity along its distribution, and its non-aggressive nature and small size make it the most heavily hunted crocodile in West and Central Africa\u003csup\u003e15,31,32\u003c/sup\u003e. The CITES also recognises the genus to be monospecific (\u003cem\u003eO. tetraspis\u003c/em\u003e), with all populations listed in Appendix I\u003csup\u003e23\u003c/sup\u003e. Hunting and human-driven habitat transformation are likely the major threats to the persistence of this taxon\u003csup\u003e30,31\u003c/sup\u003e.\u003c/p\u003e\n\u003cp\u003eAlthough crocodiles are charismatic and economically valuable keystone species, the information available on their diversity, distribution and threats in Guinea-Bissau is mostly outdated and incomplete. Recent studies confirm that \u003cem\u003eCrocodylus suchus\u003c/em\u003e is widespread across the country, while \u003cem\u003eO. cf tetraspis\u003c/em\u003e is mostly found in the south, with some scattered populations in the Cacheu region. Both species were also present in the Bijagós Archipelago, at least until 2012\u003csup\u003e27,33\u003c/sup\u003e. The presence of \u003cem\u003eM. cataphractus\u003c/em\u003e in the country has long been debated and it has been suggested that it could inhabit the coastal lagoons of Guinea-Bissau and the major watercourses in the bordering regions with Senegal and the Republic of Guinea\u003csup\u003e27\u003c/sup\u003e.\u0026nbsp;\u003c/p\u003e\n\u003cp\u003eAdditionally, two large (\u0026gt;3.5 metres total length) crocodiles appear to be responsible for the killing of three people in the Cacheu region in 2015\u003csup\u003e34\u003c/sup\u003e. Crocodile attacks on humans are not new to Guinea-Bissau, although previous records were limited to the Bijagós Archipelago\u003csup\u003e33,35\u003c/sup\u003e. A body size greater than 3.5 metres and aggressive behaviour are not expected in \u003cem\u003eC. suchus\u003c/em\u003e (Geoffroy Saint-Hilaire, 1807)\u003csup\u003e17\u003c/sup\u003e, raising the possibility that relict populations of the Nile crocodile (\u003cem\u003eCrocodylus niloticus\u003c/em\u003e) may persist in the country. \u003cem\u003eCrocodylus niloticus\u003c/em\u003e was present in West Africa in the Senegal River until at least 1803\u003csup\u003e17\u003c/sup\u003e. However, the species is now known to be extinct in the region and distributed only in eastern, central and southern Africa\u003csup\u003e22,36\u003c/sup\u003e.\u003c/p\u003e\n\u003cp\u003eThis study aims to provide updated information on the diversity, distribution, and conservation of crocodiles in Guinea-Bissau, by answering the following questions: 1) How many extant species of crocodiles occur in Guinea-Bissau? 2) How are these species spatially distributed? 3) What are the major threats to the persistence of crocodiles in the country? Using a combination of visual surveys, inquiries, molecular data, opportunistic bycatch images from camera trapping, and bibliographic review of the available information, we aim to provide new insights into how crocodile diversity is distributed across the country. Finally, by classifing threats following the guidelines established by the IUCN Red List Unified Classification of Direct Threats, we also aim to gather comprehensive information on the major threats facing these species in Guinea-Bissau.\u003c/p\u003e"},{"header":"Results","content":"\u003cdiv id=\"Sec3\" class=\"Section2\"\u003e \u003ch2\u003e3.1 Species Diversity\u003c/h2\u003e \u003cp\u003eThe probability of assignment (PI) of our query sequences to the NCBI dataset ranged from 96\u0026ndash;100%, with the first five sequences selected by BLAST as more similar to our query sequences. Query cover was always 100%. BLAST results highlighted the presence of three species among our sequences: Nile crocodile (\u003cem\u003eCrocodylus niloticus\u003c/em\u003e), West African crocodile (\u003cem\u003eCrocodylus suchus\u003c/em\u003e), and the West African dwarf crocodile (\u003cem\u003eOsteolaemus\u003c/em\u003e cf \u003cem\u003etetraspis\u003c/em\u003e). When blasting our query sequences of \u003cem\u003eC. suchus\u003c/em\u003e, among the 10 sequences selected by BLAST as the most similar to our query sequence, we had matching sequences labelled as \u003cem\u003eC. niloticus\u003c/em\u003e, although they had already been identified as belonging to \u003cem\u003eC. suchus\u003c/em\u003e in previous studies\u003csup\u003e\u003cspan citationid=\"CR17\" class=\"CitationRef\"\u003e17\u003c/span\u003e,\u003cspan citationid=\"CR37\" class=\"CitationRef\"\u003e37\u003c/span\u003e\u003c/sup\u003e.\u003c/p\u003e \u003cp\u003eAll species included in our analyses formed highly supported (\u0026gt;\u0026thinsp;99% pp) monophyletic lineages, except for the split between the \u003cem\u003eOsteolaemus\u003c/em\u003e species complex and the cluster containing the genera \u003cem\u003eCrocodylus\u003c/em\u003e and \u003cem\u003eMecistops\u003c/em\u003e (93% pp) (Fig.\u0026nbsp;\u003cspan refid=\"Fig1\" class=\"InternalRef\"\u003e1\u003c/span\u003e). The overall topology of our phylogenetic tree resembles the topology of the tree constructed by previous studies\u003csup\u003e\u003cspan citationid=\"CR17\" class=\"CitationRef\"\u003e17\u003c/span\u003e\u003c/sup\u003e. The results of our phylogenetic analyses clearly cluster two of our sequences with published sequences of \u003cem\u003eC. niloticus\u003c/em\u003e from eastern and southern Africa, 44 sequences clustering with published sequences of \u003cem\u003eC. suchus\u003c/em\u003e, and three sequences clustering with published sequences of \u003cem\u003eO. cf tetraspis\u003c/em\u003e corresponding to the new, undescribed species. Of the 44 sequences clustering with \u003cem\u003eC. suchus\u003c/em\u003e one (20795) from a sample collected in the eastern sector of the Corubal River considerably diverged within the species cluster with high support (100% pp)\u003c/p\u003e \u003cp\u003e \u003c/p\u003e \u003cp\u003eDuring our field surveys we found no evidence of \u003cem\u003eM. cataphractus\u003c/em\u003e. However, local hunters and fishermen repeatedly pointed out the presence of another \u0026ldquo;type\u0026rdquo; of crocodile, which was meticulously described as having the appearance of \u003cem\u003eC. suchus\u003c/em\u003e, but with a brownish colouration, and a longer and thinner head.\u003c/p\u003e \u003c/div\u003e \u003cdiv id=\"Sec4\" class=\"Section2\"\u003e \u003ch2\u003e3.2. Distribution\u003c/h2\u003e \u003cp\u003eWe found molecular and phenotypic (aggressive behaviour towards humans and large size) evidence for the presence of \u003cem\u003eC. niloticus\u003c/em\u003e at three sites in the western extension of Cacheu River (Fig.\u0026nbsp;\u003cspan refid=\"Fig2\" class=\"InternalRef\"\u003e2\u003c/span\u003e). One of the Cacheu River observations of \u003cem\u003eC. niloticus\u003c/em\u003e was confirmed by the successful molecular barcoding of the two individuals killed in the 2015 incident. Other two sites were found in the western Cacheu River based on recorded non-fatal crocodile attacks of unusual large crocodiles. The most recent non-fatal crocodile attack we recorded in the region occurred on the 27th of January 2025 in the western Cacheu River, where a fisherman was bitten on the right leg while exiting the water.\u003c/p\u003e \u003cp\u003e \u003c/p\u003e \u003cp\u003eWe recorded \u003cem\u003eC. suchus\u003c/em\u003e at 19 sites widely distributed across the country, mostly in the major rivers and tributaries and in fresh and brackish water lagoons. At 14 of these sites, we directly observed the species or found evidence of its presence (burrows, faeces and tracks), eight of which were confirmed by molecular identification. Two sites were found based on information from local people, and two were known from previous studies. The presence of juveniles and sub adults highlighted potentially reproducing populations in the western and eastern parts of the Cacheu River, the Geba River, the city of Bissau, the Bedasse and Cufada Lagoons, the Grande de Buba River, the Cumbidj\u0026atilde; R. tributary, the Cacine River, and the Bijag\u0026oacute;s Islands.\u003c/p\u003e \u003cp\u003eWe recorded \u003cem\u003eO. cf tetraspis\u003c/em\u003e at 15 sites distributed throughout southern Guinea-Bissau (Fig.\u0026nbsp;\u003cspan refid=\"Fig2\" class=\"InternalRef\"\u003e2\u003c/span\u003e). This species was found exclusively in small permanent or temporary rivers and pools surrounded by riparian forest, or in disturbed areas close to these sites (i.e. rice fields). We confirmed the presence of the species by direct observation of individuals in three sites, camera-traps records in eight sites, barcoding faecal samples in one site, and by bibliographical search in three sites.\u003c/p\u003e \u003c/div\u003e \u003cdiv id=\"Sec5\" class=\"Section2\"\u003e \u003ch2\u003e3.3 Conservation\u003c/h2\u003e \u003cp\u003eWe identified 13 types of threats potentially affecting crocodile populations and their habitats in 16 sites (Table\u0026nbsp;\u003cspan refid=\"Tab1\" class=\"InternalRef\"\u003e1\u003c/span\u003e). \u003cem\u003eCrocodylus suchus\u003c/em\u003e was the species affected by more threats (12), followed by \u003cem\u003eO. cf tetraspis\u003c/em\u003e (9) and \u003cem\u003eC. niloticus\u003c/em\u003e (5). Drought and persecution/control were the most recorded threats, followed by pollution from garbage, and solid waste and soap. However, most of the threats recorded (10) have as consequence habitat loss and/or degradation. Of the threats involving direct killing of crocodiles, all the records were classified as pas, the six related to persecution/control were classified as likely to repeat, while the four related to war, and military exercises as unlikely to repeat.\u003c/p\u003e \u003cp\u003e \u003cdiv class=\"gridtable\"\u003e\u003ctable float=\"Yes\" id=\"Tab1\" border=\"1\"\u003e \u003ccaption language=\"En\"\u003e \u003cdiv class=\"CaptionNumber\"\u003eTable 1\u003c/div\u003e \u003cdiv class=\"CaptionContent\"\u003e \u003cp\u003eConservation threats identified in this study for crocodiles in Guinea-Bissau. The table includes threat code, definition, species affected, number and percentage of sites where the threat has been observed (total number of sites\u0026thinsp;=\u0026thinsp;19). Letters in the Species column stand for: \u0026ldquo;n\u0026rdquo; \u003cem\u003eC. niloticus\u003c/em\u003e, \u0026ldquo;s\u0026rdquo; \u003cem\u003eC. suchus\u003c/em\u003e, \u0026ldquo;t\u0026rdquo; \u003cem\u003eOsteolaemus cf tetraspis\u003c/em\u003e. Coding and description are based on the IUCN Red List classification scheme.\u003c/p\u003e \u003c/div\u003e \u003c/caption\u003e \u003ccolgroup cols=\"4\"\u003e \u003cdiv align=\"left\" class=\"colspec\" colname=\"c1\" colnum=\"1\"\u003e\u003c/div\u003e \u003cdiv align=\"left\" class=\"colspec\" colname=\"c2\" colnum=\"2\"\u003e\u003c/div\u003e \u003cdiv align=\"left\" class=\"colspec\" colname=\"c3\" colnum=\"3\"\u003e\u003c/div\u003e \u003cdiv align=\"left\" class=\"colspec\" colname=\"c4\" colnum=\"4\"\u003e\u003c/div\u003e \u003cthead\u003e \u003ctr\u003e \u003cth align=\"left\" colname=\"c1\"\u003e \u003cp\u003eCode\u003c/p\u003e \u003c/th\u003e \u003cth align=\"left\" colname=\"c2\"\u003e \u003cp\u003eThreats\u003c/p\u003e \u003c/th\u003e \u003cth align=\"left\" colname=\"c3\"\u003e \u003cp\u003eSpecies\u003c/p\u003e \u003c/th\u003e \u003cth align=\"left\" colname=\"c4\"\u003e \u003cp\u003eN of sites (%)\u003c/p\u003e \u003c/th\u003e \u003c/tr\u003e \u003c/thead\u003e \u003ctbody\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e \u003cp\u003e1.1\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003eHousing \u0026amp; urban areas\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e \u003cp\u003en, s, t\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c4\"\u003e \u003cp\u003e3 (15.7)\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e \u003cp\u003e1.2\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003eCommercial \u0026amp; industrial areas\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e \u003cp\u003en, s, t\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c4\"\u003e \u003cp\u003e3 (15.7)\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e \u003cp\u003e2.1.1\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003eShifting agriculture\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e \u003cp\u003en, s, t\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c4\"\u003e \u003cp\u003e4 (21)\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e \u003cp\u003e2.3.1\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003eNomadic grazing\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e \u003cp\u003es, t\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c4\"\u003e \u003cp\u003e1 (5)\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e \u003cp\u003e2.3.2\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003eSmall-holder grazing, ranching or farming\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e \u003cp\u003es, t\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c4\"\u003e \u003cp\u003e3 (15.7)\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e \u003cp\u003e3.2\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003eMining \u0026amp; quarrying\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e \u003cp\u003es\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c4\"\u003e \u003cp\u003e1 (5)\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e \u003cp\u003e5.4.3\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003eIncidental or accidental mortality (bycatch - subsistence/small scale)\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e \u003cp\u003es, t\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c4\"\u003e \u003cp\u003e3 (15.7)\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e \u003cp\u003e5.4.5\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003ePersecution/control\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e \u003cp\u003en, s\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c4\"\u003e \u003cp\u003e6 (31.5)\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e \u003cp\u003e6.2\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003eWar, civil unrest \u0026amp; military exercises\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e \u003cp\u003es, t\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c4\"\u003e \u003cp\u003e4 (21)\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e \u003cp\u003e9.1.1\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003eSewage\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e \u003cp\u003es\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c4\"\u003e \u003cp\u003e2 (10.5)\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e \u003cp\u003e9.1.3\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003eType Unknown/Unrecorded (Detergents)\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e \u003cp\u003es\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c4\"\u003e \u003cp\u003e5 (26.3)\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e \u003cp\u003e9.4\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003eGarbage \u0026amp; solid waste\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e \u003cp\u003es, t\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c4\"\u003e \u003cp\u003e6 (31.5)\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e \u003cp\u003e11.2\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003eDroughts\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e \u003cp\u003et\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c4\"\u003e \u003cp\u003e7 (36.8)\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003c/tbody\u003e \u003c/colgroup\u003e \u003c/table\u003e\u003c/div\u003e \u003c/p\u003e \u003cp\u003eThe two confirmed observations of \u003cem\u003eC. niloticus\u003c/em\u003e come from two individuals killed by local authorities in 2015 because they were suspected of having eaten three people during the rainy season. Another possible \u003cem\u003eC. niloticus\u003c/em\u003e (without molecular confirmation) was killed a few days later for the same reason at a second site in the Cacheu River. No retaliation events had followed the last human-crocodile incident that occurred on the 27th of January 2025 in the western Cacheu River. The four observations related to war, and military exercises come from the online resources. Specifically, they are three records of adults and sub-adults of either \u003cem\u003eC. niloticus\u003c/em\u003e or \u003cem\u003eC. suchus\u003c/em\u003e killed by the Portuguese military for bushmeat or during military operations between the years 1967 and 1974, and one \u003cem\u003eO. cf tetraspis\u003c/em\u003e also captured by the Portuguese military around 1973\u0026ndash;1974, all during the colonial period\u003csup\u003e\u003cspan citationid=\"CR34\" class=\"CitationRef\"\u003e34\u003c/span\u003e\u003c/sup\u003e. Inquiry data indicated that although crocodiles are occasionally eaten, they are not actively hunted for meat consumption, but their body parts are used in the production of goods (e.g., bags), traditional medicine and fetish rituals. One observation of \u003cem\u003eC. suchus\u003c/em\u003e and one of \u003cem\u003eO. cf tetraspis\u003c/em\u003e were from individuals which accidentally died in fishing nets in the Cacheu River and in Bel\u0026iacute; (respectively).\u003c/p\u003e \u003cp\u003eDomestic garbage (e.g., single-use water plastic bags) is found throughout the country, but it is particularly prevalent in urban and suburban areas. In these areas, streams, drainage channels and rice fields are filled with plastic and other degradable and non-degradable waste, from animal carcasses to discarded appliances. Pollution from soap was mainly observed in urban areas where people gather around large water bodies (e.g., in Saltinho, in the Corubal River or the mangrove forest in Bissau) to wash clothes, cars and themselves. Pollution from sewage was just recorded in Bissau.\u003c/p\u003e \u003cp\u003eWe recorded evidence of land conversion, habitat degradation, and overexploitation of natural resources in the form of urban expansion, quarry mining activities near major riverbanks, shifting (slash-and-burn) agriculture, and nomadic and non-nomadic grazing. Quarry mining, and slash-and-burn agriculture were mainly recorded along the Corubal River, while nomadic and non-nomadic grazing was mostly recorded around freshwater lagoons (\u003cem\u003ewendus\u003c/em\u003e). The intensifying land conversion recorded is particularly due to the increasing permanent habitat change from rainfed shifting agriculture to cashew orchards, as for instance along the Balana River.\u003c/p\u003e \u003cp\u003eClimate change was only identified as a potential threat to \u003cem\u003eO. cf tetraspis\u003c/em\u003e, as most of the remnant river pools where the species has been observed may disappear in the future if the extent of the dry season increases\u003csup\u003e\u003cspan citationid=\"CR38\" class=\"CitationRef\"\u003e38\u003c/span\u003e\u003c/sup\u003e.\u003c/p\u003e \u003c/div\u003e"},{"header":"Discussion","content":"\u003cp\u003eOur study gathers evidence of the presence of three crocodile species in Guinea-Bissau, distributed both on the mainland and in the Bijag\u0026oacute;s Archipelago. We have also highlighted the major threats to each species based on the IUCN Red List classification scheme. These threats are related to habitat loss, degradation, and direct killing of crocodiles.\u003c/p\u003e \u003cdiv id=\"Sec7\" class=\"Section2\"\u003e \u003ch2\u003e4.1. Species Diversity and distribution\u003c/h2\u003e \u003cp\u003eThe molecular barcoding of samples collected from two crocodiles killed by local authorities in the region of Cacheu during a culling operation in 2015, provide strong evidence the presence of \u003cem\u003eC. niloticus\u003c/em\u003e in West Africa after the last confirmed observation 222 years ago\u003csup\u003e\u003cspan citationid=\"CR17\" class=\"CitationRef\"\u003e17\u003c/span\u003e\u003c/sup\u003e. These two crocodiles of 3.5 and 5 metres (full body length) were believed to be responsible for repeated attacks on pirogues and people during the 2015 rainy season, resulting in three fatalities and multiple injuries\u003csup\u003e\u003cspan citationid=\"CR34\" class=\"CitationRef\"\u003e34\u003c/span\u003e\u003c/sup\u003e. During our field expeditions surveys, we were also informed of the presence of large individuals (\u0026gt;\u0026thinsp;5 metres) on the island of Imbone, in the Bijag\u0026oacute;s Archipelago (Miguel Lecoq personal observation). Human-crocodile conflicts were common in the Bijag\u0026oacute;s Archipelago in the past, often resulting in fatal encounters\u003csup\u003e\u003cspan citationid=\"CR35\" class=\"CitationRef\"\u003e35\u003c/span\u003e\u003c/sup\u003e. The attacks on humans and the large body size also suggest the presence of \u003cem\u003eC. niloticus\u003c/em\u003e on the islands. This species was last confirmed in West Africa in 1803 in the Senegal River\u003csup\u003e\u003cspan citationid=\"CR17\" class=\"CitationRef\"\u003e17\u003c/span\u003e\u003c/sup\u003e. Until now, \u003cem\u003eC. niloticus\u003c/em\u003e was thought extinct in the region, with \u003cem\u003eC. suchus\u003c/em\u003e considered the sole species of the genus \u003cem\u003eCrocodylus\u003c/em\u003e\u003csup\u003e\u003cspan citationid=\"CR17\" class=\"CitationRef\"\u003e17\u003c/span\u003e,\u003cspan additionalcitationids=\"CR21\" citationid=\"CR20\" class=\"CitationRef\"\u003e20\u003c/span\u003e\u0026ndash;\u003cspan citationid=\"CR22\" class=\"CitationRef\"\u003e22\u003c/span\u003e\u003c/sup\u003e. Due to the lack of an accepted dichotomous key to distinguish \u003cem\u003eC. niloticus\u003c/em\u003e from \u003cem\u003eC. suchus\u003c/em\u003e morphologically, attacks in the Cacheu region (and the few other attacks by crocodiles of the genus \u003cem\u003eCrocodylus\u003c/em\u003e in West Africa) were attributed to \u003cem\u003eC. suchus\u003c/em\u003e (\u003cspan class=\"ExternalRef\"\u003e\u003cspan class=\"RefSource\"\u003ehttps://crocattack.org/database/\u003c/span\u003e\u003cspan address=\"https://crocattack.org/database/\" targettype=\"URL\" class=\"RefTarget\"\u003e\u003c/span\u003e\u003c/span\u003e\u003cspan type=\"Underline\" class=\"Underline\" name=\"Emphasis\"\u003e).\u003c/span\u003e However, our mitochondrial DNA analysis indicates that \u003cem\u003eC. niloticus\u003c/em\u003e is likely responsible for the reported attacks on humans in the Cacheu region.\u003c/p\u003e \u003cp\u003eTo date, no comprehensive public study has compared the phenotypic traits of these two species, making it urgent to investigate potential morphological and behavioural differences. Establishing clear dichotomous characters would improve field identification and aid conservation efforts. Although our morphological, behavioral, and genetic evidence strongly supports the presence of \u003cem\u003eC. niloticus\u003c/em\u003e in the area, our analysis is based on a fragment of mtDNA. We cannot rule out the possibility that we are detecting \u003cem\u003eC. niloticus\u003c/em\u003e mitochondrial introgression in \u003cem\u003eC. suchus\u003c/em\u003e, which, if confirmed, would represent the first documented case of hybridization between the two species in the wild. Therefore, future studies using nuclear molecular markers are urgently needed to confirm the presence of \u003cem\u003eC. niloticus\u003c/em\u003e populations in Guinea-Bissau and potentially in neighbouring countries such as the Republic of Guinea, where attacks have also been recorded (\u003cspan class=\"ExternalRef\"\u003e\u003cspan class=\"RefSource\"\u003ehttps://crocattack.org/database/\u003c/span\u003e\u003cspan address=\"https://crocattack.org/database/\" targettype=\"URL\" class=\"RefTarget\"\u003e\u003c/span\u003e\u003c/span\u003e). These areas should be promptly protected to ensure safe coexistence between human and crocodile populations.\u003c/p\u003e \u003cp\u003eOur results confirm the presence of \u003cem\u003eOsteolaemus tetraspis sensu lato\u003c/em\u003e in Guinea-Bissau, both on the mainland and in the Bijag\u0026oacute;s Archipelago. Our molecular identification analyses place the barcoded samples within the same clade as the undescribed lineage \u003cem\u003eOsteolaemus. cf tetraspis\u003c/em\u003e from West Africa. This clade has already been shown to be genetically divergent from the other two species of \u003cem\u003eOsteolaemus\u003c/em\u003e (\u003cem\u003eO. tetraspis sensu stricto\u003c/em\u003e and \u003cem\u003eO. osborni\u003c/em\u003e)\u003csup\u003e\u003cspan citationid=\"CR26\" class=\"CitationRef\"\u003e26\u003c/span\u003e\u003c/sup\u003e. \u003cem\u003eOsteolaemus. cf tetraspis\u003c/em\u003e was (and still is) locally widely confused with the neotropical species of caimans and is commonly referred to by the non-scientific community as \"\u003cem\u003ejacar\u0026eacute;\u003c/em\u003e\" (caiman in Brazilian Portuguese)\u003csup\u003e\u003cspan citationid=\"CR34\" class=\"CitationRef\"\u003e34\u003c/span\u003e\u003c/sup\u003e. Caimans (Caimaninae; Brochu, 1999) are small to medium-sized crocodilian reptiles of the family Alligatoridae Gray 1844, native to Central and South America. These species belong to the genera \u003cem\u003eCaiman\u003c/em\u003e, \u003cem\u003eMelanosuchus\u003c/em\u003e, and \u003cem\u003ePaleosuchus\u003c/em\u003e, none of which have their natural distribution in Africa; therefore, no caiman (\u003cem\u003ejacar\u0026eacute;\u003c/em\u003e) species occur naturally in Guinea-Bissau.\u003c/p\u003e \u003cp\u003eOur observations of \u003cem\u003eO. cf tetraspis\u003c/em\u003e are restricted to southern Guinea-Bissau and the Bijag\u0026oacute;s Archipelago. Based on the available literature\u003csup\u003e\u003cspan citationid=\"CR27\" class=\"CitationRef\"\u003e27\u003c/span\u003e\u003c/sup\u003e, the distribution of \u003cem\u003eO. cf tetraspis\u003c/em\u003e should extend to northern Guinea-Bissau, south of Senegal and The Gambia. However, there are no recent observations of the species in southern Senegal (Casamance region), while the species was thought to be extinct in The Gambia prior to 2010\u003csup\u003e39\u003c/sup\u003e, when breeding populations were discovered\u003csup\u003e\u003cspan citationid=\"CR27\" class=\"CitationRef\"\u003e27\u003c/span\u003e\u003c/sup\u003e. The lack of updated observations and the increasing anthropization and land cover changes that have affected West Africa in recent decades\u003csup\u003e\u003cspan additionalcitationids=\"CR41\" citationid=\"CR40\" class=\"CitationRef\"\u003e40\u003c/span\u003e\u0026ndash;\u003cspan citationid=\"CR42\" class=\"CitationRef\"\u003e42\u003c/span\u003e\u003c/sup\u003e may have restricted the current global distribution of \u003cem\u003eO.\u003c/em\u003e cf \u003cem\u003etetraspis\u003c/em\u003e to southern Guinea-Bissau and likely the Republic of Guinea, with possible isolated populations in The Gambia. There is an urgent need to survey the western limit of this species distribution and to assess whether \u003cem\u003eO. cf tetraspis\u003c/em\u003e still persists in southern Senegal and northern Guinea-Bissau, and to assess the status of the remaining populations.\u003c/p\u003e \u003cp\u003eDuring our field surveys, we found no direct evidence of the presence of \u003cem\u003eMecistops cataphractus\u003c/em\u003e. However, local hunters and fishermen consistently described sightings of a crocodile resembling \u003cem\u003eC. suchus\u003c/em\u003e but with a brownish coloration and a longer, thinner head. These repeated accounts, along with numerous observations of unusually shaped crocodiles\u0026mdash;especially in the south\u0026mdash;raise intriguing questions about the possible presence of \u003cem\u003eM. cataphractus\u003c/em\u003e or unrecognized morphological variations. Notably, the presence of this species in the region was previously highlighted\u003csup\u003e\u003cspan citationid=\"CR27\" class=\"CitationRef\"\u003e27\u003c/span\u003e\u003c/sup\u003e, further supporting the need for targeted investigations to clarify \u003cem\u003eM. cataphractus\u003c/em\u003e presence in Guinea-Bissau.\u003c/p\u003e \u003c/div\u003e \u003cdiv id=\"Sec8\" class=\"Section2\"\u003e \u003ch2\u003e4.2. Conservation threats\u003c/h2\u003e \u003cp\u003eMost of the threats recorded during our expeditions were led to habitat loss and/or degradation. However, the most frequently observed were droughts and direct crocodile persecution. Although crocodiles are fully protected by CITES and Guinea-Bissau wildlife law\u003csup\u003e\u003cspan citationid=\"CR23\" class=\"CitationRef\"\u003e23\u003c/span\u003e\u003c/sup\u003e, crocodile body parts remain a valuable commodity in Guinea-Bissau. Although we do not have evidence that crocodile hunting still occurs in Guinea-Bissau few hunters actively hunt them using non-automatic firearms, spears or land traps (i.e. snares) until recently\u003csup\u003e\u003cspan citationid=\"CR35\" class=\"CitationRef\"\u003e35\u003c/span\u003e\u003c/sup\u003e. Although of uknown origin, \u003cem\u003eO. cf tetraspis\u003c/em\u003e, body parts were the most abundant crocodile items at the Bandim market in Bissau, the capital city, even surpassing those of \u003cem\u003eC. suchus\u003c/em\u003e (CP personal observation). Due to its small size and tame behaviour, \u003cem\u003eO. cf tetraspis\u003c/em\u003e is highly traded throughout its distribution\u003csup\u003e\u003cspan citationid=\"CR31\" class=\"CitationRef\"\u003e31\u003c/span\u003e,\u003cspan citationid=\"CR32\" class=\"CitationRef\"\u003e32\u003c/span\u003e,\u003cspan citationid=\"CR43\" class=\"CitationRef\"\u003e43\u003c/span\u003e\u003c/sup\u003e. Overhunting can lead to extinction, and disrupt population dynamics and activity patterns\u003csup\u003e\u003cspan citationid=\"CR44\" class=\"CitationRef\"\u003e44\u003c/span\u003e,\u003cspan citationid=\"CR45\" class=\"CitationRef\"\u003e45\u003c/span\u003e\u003c/sup\u003e, while unregulated bushmeat trade and consumption can increase the risk of zoonotic diseases\u003csup\u003e\u003cspan citationid=\"CR46\" class=\"CitationRef\"\u003e46\u003c/span\u003e,\u003cspan citationid=\"CR47\" class=\"CitationRef\"\u003e47\u003c/span\u003e\u003c/sup\u003e. However, little is still known on the extent of crocodile trade in Guinea-Bissau, nor on the socio-economic drivers behind the trade in crocodile body parts. Additionally, the lack of information on population size, distribution, and trends\u0026mdash;both current and historical\u0026mdash;combined with the uncertainty surrounding the scale of the trade, poses a serious threat to the species' persistence in the country. Urgent studies are needed to fill these knowledge gaps, strengthen conservation efforts, and prevent the silent disappearance of this still-undescribed species from Guinea-Bissau.\u003c/p\u003e \u003cp\u003eThe direct killing of crocodiles in Guinea-Bissau has mostly been driven by persecution due to human-crocodile conflict and, historically, by warfare. Crocodile hunting in Guinea-Bissau was intense during the colonial period, including with the use of automatic machine guns and grenades, and was often carried out by the Portuguese military, who had easy access to firearms\u003csup\u003e\u003cspan citationid=\"CR34\" class=\"CitationRef\"\u003e34\u003c/span\u003e\u003c/sup\u003e. Human-wildlife conflicts can be driven by several factors including climate change\u003csup\u003e\u003cspan citationid=\"CR48\" class=\"CitationRef\"\u003e48\u003c/span\u003e\u003c/sup\u003e and the intensification of environmental stressors, such as land conversion, habitat degradation, and overexploitation of natural resources\u003csup\u003e\u003cspan additionalcitationids=\"CR50\" citationid=\"CR49\" class=\"CitationRef\"\u003e49\u003c/span\u003e\u0026ndash;\u003cspan citationid=\"CR51\" class=\"CitationRef\"\u003e51\u003c/span\u003e\u003c/sup\u003e. The human population of Guinea-Bissau has grown by approximately 120% from 1990 to 2024\u003csup\u003e52\u003c/sup\u003e, intensifying environmental pressure. This has led to habitat loss due to urban expansion and commodity crop cultivation\u003csup\u003e\u003cspan citationid=\"CR53\" class=\"CitationRef\"\u003e53\u003c/span\u003e\u003c/sup\u003e, as well as habitat degradation caused by chemical pollution (e.g., domestic detergents) and slash-and-burn agriculture\u003csup\u003e\u003cspan citationid=\"CR54\" class=\"CitationRef\"\u003e54\u003c/span\u003e\u003c/sup\u003e. These changes likely exacerbate the risk of human-crocodile conflict and can result in direct disturbance and reduction of reproductive opportunities, for example through the destruction of nesting and nursery habitats (i.e. sandbanks and mangroves). The use of fire in slash-and-burn agriculture to clear natural patches of riparian forest along the Corubal River is another example. The degradation and depletion of riparian forests may lead to the rapid extinction of \u003cem\u003eO. cf tetraspis\u003c/em\u003e\u003csup\u003e\u003cspan citationid=\"CR43\" class=\"CitationRef\"\u003e43\u003c/span\u003e\u003c/sup\u003e, which depends on the persistence of these forested environments\u003csup\u003e\u003cspan citationid=\"CR55\" class=\"CitationRef\"\u003e55\u003c/span\u003e\u003c/sup\u003e. The increase in nomadic and non-nomadic grazing, particularly around freshwater lagoons (\u003cem\u003ewendus\u003c/em\u003e), also poses a threat to the persistence of crocodiles as it may lead to water shortage and pollution\u003csup\u003e\u003cspan citationid=\"CR56\" class=\"CitationRef\"\u003e56\u003c/span\u003e\u003c/sup\u003e. Finally, if the length of the dry season increases as predicted\u003csup\u003e\u003cspan citationid=\"CR38\" class=\"CitationRef\"\u003e38\u003c/span\u003e\u003c/sup\u003e suitable habitat for \u003cem\u003eO. cf tetraspis\u003c/em\u003e might also disappear in the near future. Holistic approaches, such as agroecology, could be valuable in addressing human-wildlife conflict while implementing sustainable farming and wildlife management\u003csup\u003e\u003cspan citationid=\"CR57\" class=\"CitationRef\"\u003e57\u003c/span\u003e\u003c/sup\u003e. There is an urgent need to strengthen national and sub-national policies on habitat protection and pollution control, alongside implementing projects that promote habitat restoration and raise awareness of the importance of conserving natural ecosystems. These efforts will be crucial to mitigating the possible negative impacts of advancing climate change.\u003c/p\u003e \u003c/div\u003e"},{"header":"Conservation management and future research","content":"\u003cp\u003eBased on our findings, there is a critical need for comprehensive conservation management and research to address the lack of knowledge about crocodiles in Guinea-Bissau and the threats they are facing. As unassessed biodiversity is more likely to go extinct\u003csup\u003e\u003cspan citationid=\"CR58\" class=\"CitationRef\"\u003e58\u003c/span\u003e\u003c/sup\u003e, the taxonomic clarification of the genus \u003cem\u003eOsteolaemus\u003c/em\u003e is urgently needed to inform and guide conservation efforts for the species in Guinea-Bissau and neighbouring countries. Future research should focus on standardized and systematic monitoring of known crocodile populations, their habitats, and trade trends, all of which are essential for more effective conservation measures. Moreover, future research should focus on the codification of dichotomous morphological characters to distinguish \u003cem\u003eC. suchus\u003c/em\u003e and \u003cem\u003eC. niloticus\u003c/em\u003e, as well as the use of molecular methods to confirm species identification and investigate the presence of \u003cem\u003eC. niloticus\u003c/em\u003e in surrounding regions where human-crocodile conflicts are also occurring (e.g., Republic of Guinea). Additionally, the presence of \u003cem\u003eM. cataphractus\u003c/em\u003e in Guinea-Bissau remains uncertain, despite reports from local hunters and fishermen describing crocodiles with distinct morphological traits. Given these accounts and previous indications\u003csup\u003e\u003cspan citationid=\"CR27\" class=\"CitationRef\"\u003e27\u003c/span\u003e\u003c/sup\u003e, further research is needed to clarify crocodile diversity in the region.\u003c/p\u003e \u003cp\u003eConservation actions should focus on site and habitat protection, area management, and restoration of natural processes that have been lost, especially in areas critical for the survival of \u003cem\u003eO. cf tetraspis\u003c/em\u003e (i.e., urban areas in the northwest of the country), and to facilitate the coexistence of the human population with the potentially vulnerable populations of \u003cem\u003eC. niloticus\u003c/em\u003e. Maintaining the protection of sacred forests has proved to be important for crocodiles\u003csup\u003e\u003cspan citationid=\"CR59\" class=\"CitationRef\"\u003e59\u003c/span\u003e\u003c/sup\u003e. Although shifts in religious beliefs in Guinea-Bissau are affecting traditional practices and the preservation of sacred forests, community-managed forests are increasingly valued in the country\u003csup\u003e\u003cspan citationid=\"CR60\" class=\"CitationRef\"\u003e60\u003c/span\u003e\u003c/sup\u003e, offering a promising solution for local crocodile conservation. Initiatives like F\u0026eacute;d\u0026eacute;ration KAFO in Djalicunda (\u003cspan class=\"ExternalRef\"\u003e\u003cspan class=\"RefSource\"\u003ehttps://kafobissau.org/en/\u003c/span\u003e\u003cspan address=\"https://kafobissau.org/en/\" targettype=\"URL\" class=\"RefTarget\"\u003e\u003c/span\u003e\u003c/span\u003e) and CHIMBO in Bel\u0026iacute; (\u003cspan class=\"ExternalRef\"\u003e\u003cspan class=\"RefSource\"\u003ehttps://www.chimbo.org\u003c/span\u003e\u003cspan address=\"https://www.chimbo.org\" targettype=\"URL\" class=\"RefTarget\"\u003e\u003c/span\u003e\u003c/span\u003e) promote wildlife conservation through research and sustainable agroecological practices, preserving natural and cultural heritage, protecting climate-resilient ecosystems, and empowering young people to safeguard the environment. Combining community-based approaches with management strategies based on genetic research and trade regulation is essential to preserve genetic diversity and mitigate exploitation risks. Enhancing education, training, and community awareness will further reduce human-crocodile conflicts and promote crocodile conservation through biodiversity-friendly practices.\u003c/p\u003e"},{"header":"Materials and Methods","content":"\u003cdiv id=\"Sec11\" class=\"Section2\"\u003e \u003ch2\u003e2.1. Study area\u003c/h2\u003e \u003cp\u003eGuinea-Bissau, located in West Africa, is bordered by Senegal, the Republic of Guinea, and the Atlantic Ocean (Fig.\u0026nbsp;\u003cspan refid=\"Fig3\" class=\"InternalRef\"\u003e3\u003c/span\u003e). It covers 36,125 km\u0026sup2;, with a population of about 2.1 million\u003csup\u003e\u003cspan citationid=\"CR52\" class=\"CitationRef\"\u003e52\u003c/span\u003e\u003c/sup\u003e. The country features two main ecoregions: the Guinean forest-savannah mosaic and Guinean mangroves. The landscape includes scattered coastal plains, estuaries lined with mangroves, a low-elevation mosaic of dense and open forests, and savannah woodland with a peak at 310 m in the southeast. The Bijag\u0026oacute;s Archipelago comprises 88 islands, 20 of which are permanently inhabited. The monsoonal tropical climate has a dry season (November\u0026ndash;May) and a wet season (June\u0026ndash;October), with annual rainfall ranging from 1,500 to 3,000 mm. Vegetation includes mangroves, palm groves, wet grasslands, dry open forest, savanna woodland, dense primary and secondary forest in relict patches, and riverine galleries. The main river basins in the country are the Cacheu in the north, the Mansoa and the Geba in the centre, and the Corubal in the south (Fig.\u0026nbsp;\u003cspan refid=\"Fig3\" class=\"InternalRef\"\u003e3\u003c/span\u003e).\u003c/p\u003e \u003cp\u003e \u003c/p\u003e \u003c/div\u003e \u003cdiv id=\"Sec12\" class=\"Section2\"\u003e \u003ch2\u003e2.2. Data collection\u003c/h2\u003e \u003cp\u003eWe visited the country during three expeditions, between 2021 and 2023. The expeditions were conducted in November/December 2021 (dry season), October/November 2022 (late rainy season, early dry season), and late April/May 2023 (dry season), for a total of 74 survey-days. During these expeditions we visited the mainland\u0026rsquo;s protected areas and most of the main rivers: Cacheu, Corubal, Geba, and Mansoa, as well as smaller tributaries and temporary rainfed lagoons (locally known as \u003cem\u003ewendus\u003c/em\u003e) (Fig.\u0026nbsp;\u003cspan refid=\"Fig3\" class=\"InternalRef\"\u003e3\u003c/span\u003e).\u003c/p\u003e \u003cp\u003eData were collected by: 1) visual surveys; 2) opportunistic sampling of genetic material (faeces and tissues) along rivers, lagoons, and other water bodies; 3) opportunistic bycatch camera-trapping data from eight sites in the south of the country, from a project aimed to survey forest elephants from 2020 to 2024\u003csup\u003e61\u003c/sup\u003e; 4) opportunistic presence data from interviewing knowledgeable local people (i.e. natural guides, park rangers, hunters, shepherds, and fishermen); 5) occasional visits to bushmeat and fetish markets in Bissau where we counted the number of stalls displaying items made from crocodile body parts and tried to estimate an approximate total number of such items made from crocodile body parts; 6) bibliographic review of the available scientific and non-scientific literature. We reached survey and sampling sites by car and where possible, by canoe, accompanied by local guides, park rangers or fishermen. During boat trips, we counted individuals and collected evidence of crocodile presence (i.e. faeces, tracks and burrows). We conducted day and night visual surveys from canoes. During the canoe surveys we navigated along water bodies, with two to four people spotting live individuals or evidence of crocodile presence. Where navigation was not possible (e.g. small pools along temporary rivers under riparian forest), we reached the water bodies by car or on foot and then walked along and inside them at random. Tissue samples were collected from dead individuals killed by humans. Faecal samples were collected using sterile, disposable throat inspection wooden sticks. Tissue samples were stored in 96% ethanol until DNA extraction, while faecal samples were stored in 50ml Falcon tubes filled with sterile silica gel. The geographic location of each observation or genetic sample was recorded using a Global Positioning System (GPS) device. All methods were carried out in accordance with relevant guidelines and regulations. Fieldwork and data collection were conducted with permission from IBAP. Interviews were informal, unstructured, and anonymous, and responses were kept confidential. Informed consent was obtained from all participants involved in the study.\u003c/p\u003e \u003cp\u003eWe also recorded threats that may affect crocodiles in the country and classified them based on the Unified Classification of Direct Threats Version 3.3 provided by the IUCN Red List\u003csup\u003e\u003cspan citationid=\"CR62\" class=\"CitationRef\"\u003e62\u003c/span\u003e\u003c/sup\u003e.\u003c/p\u003e \u003c/div\u003e \u003cdiv id=\"Sec13\" class=\"Section2\"\u003e \u003ch2\u003e2.3. Molecular identification\u003c/h2\u003e \u003cp\u003eFor DNA extraction, we followed\u003csup\u003e\u003cspan citationid=\"CR20\" class=\"CitationRef\"\u003e20\u003c/span\u003e\u003c/sup\u003e. We extracted DNA from tissues samples using the DNeasy Blood \u0026amp; Tissue Kit (QIAGEN) and from faecal samples using the GuSCN/silica method\u003csup\u003e\u003cspan citationid=\"CR63\" class=\"CitationRef\"\u003e63\u003c/span\u003e\u003c/sup\u003e. For faecal samples we performed extraction and pre-PCR procedures at BIOPOLIS-CIBIO research centre in dedicated low-quality DNA facilities, sterilised and equipped with positive air pressure and UV lights.\u003c/p\u003e \u003cp\u003eFor DNA barcoding analyses we amplified a 421 base pair (bp) 12S mitochondrial DNA (mtDNA) fragment in 10 \u0026micro;l reaction volume, containing 5 \u0026micro;l of master mix (Multiplex PCR Kit, QIAGEN), 0.5 uM of each primer and between 1 and 2 \u0026micro;l of DNA for tissue and faecal samples, respectively. Primer information and PCR conditions were the same as in Table S2 of Velo-Anton \u003cem\u003eet al.\u003c/em\u003e (2014). We performed cycle sequencing for both strands using PCR primers and the ABI PRISM BigDye Terminator kit (AB Applied Biosystems) in a MyCycler BioRad Thermal Cycler and sequenced PCR products on an ABI 3130xl Genetic Analyzer (AB Applied Biosystems).\u003c/p\u003e \u003cp\u003eWe checked and edited electropherograms by eye and aligned all sequences using GENEIOUS PRIME 2024.0.7. We then downloaded available 12S sequences of \u003cem\u003eCrocodylus niloticus, C. suchus\u003c/em\u003e, \u003cem\u003eC. porosus\u003c/em\u003e (Schneider, 1801), \u003cem\u003eOsteolaemus osborni, O. tetraspis, O. cf tetraspis, Mecistops cataphractus, M. leptorhynchus, Gavialis gangeticus\u003c/em\u003e (Gmelin, 1789), \u003cem\u003eTomistoma schlegelii\u003c/em\u003e (M\u0026uuml;ller, 1838) from previous publications\u003csup\u003e\u003cspan citationid=\"CR20\" class=\"CitationRef\"\u003e20\u003c/span\u003e,\u003cspan citationid=\"CR26\" class=\"CitationRef\"\u003e26\u003c/span\u003e,\u003cspan citationid=\"CR37\" class=\"CitationRef\"\u003e37\u003c/span\u003e,\u003cspan additionalcitationids=\"CR65\" citationid=\"CR64\" class=\"CitationRef\"\u003e64\u003c/span\u003e\u0026ndash;\u003cspan citationid=\"CR66\" class=\"CitationRef\"\u003e66\u003c/span\u003e\u003c/sup\u003e.\u003c/p\u003e \u003cp\u003eThe final alignment contains a total of 142 sequences with a length of 313 bp. The first step of our species identification was performed in BLASTn (\u003cspan class=\"ExternalRef\"\u003e\u003cspan class=\"RefSource\"\u003ehttps://blast.ncbi.nlm.nih.gov/Blast.cgi\u003c/span\u003e\u003cspan address=\"https://blast.ncbi.nlm.nih.gov/Blast.cgi\" targettype=\"URL\" class=\"RefTarget\"\u003e\u003c/span\u003e\u003c/span\u003e\u003cspan type=\"Underline\" class=\"Underline\" name=\"Emphasis\"\u003e)\u003c/span\u003e to compare our query sequences with the NCBI reference sequence database. Sequences were identified at the species level when the percentage of identification was higher than 96% for the first 10 matching sequences in the NCBI database. Since some available sequences from \u003cem\u003eC. suchus\u003c/em\u003e are still named as \u003cem\u003eC. niloticus\u003c/em\u003e in the NCBI database, we performed a Bayesian inference analysis using BEAST 2.5\u003csup\u003e67\u003c/sup\u003e to establish the correct phylogenetic position of our sequences from the three genera. We run three separate analyses, each for 10\u003csup\u003e7\u003c/sup\u003e generations with sampling at every 10\u003csup\u003e3\u003c/sup\u003e MCMC steps. We used the strict clock model and the Coalescent Constant Population prior. We used IQ-TREE\u003csup\u003e\u003cspan citationid=\"CR68\" class=\"CitationRef\"\u003e68\u003c/span\u003e\u003c/sup\u003e to infer the model to be assigned to the appropriate partitions. We used Tracer V1.7.2\u003csup\u003e69\u003c/sup\u003e to visualise the log file of each run and summarise the analytic statistics. The effective sample size was sufficient for all statistics (ESS\u0026thinsp;\u0026gt;\u0026thinsp;200). We then used LogCombiner to combine the tree files from each run discarding a 10% burn-in. We used TreeAnnotator to produce the maximum credibility tree and annotate the 95% highest probability density ranges.\u003c/p\u003e \u003c/div\u003e"},{"header":"Declarations","content":"\u003cp\u003e\u003cstrong\u003eAcknowledgments\u0026nbsp;\u003c/strong\u003e\u003c/p\u003e\n\u003cp\u003eWe would like to acknowledge the Guinea-Bissau governmental agency Instituto de Biodiversidade e \u0026Aacute;reas Protegidas (IBAP), namely the former director Dr. Justino Biai for fieldwork and sampling permits. We are grateful to the CHIMBO NGO, Ana Rainho and her research team, the workers of the NGO KAFO (Guinea-Bissau), and to the people of Djalicunda, Farim and all the tabanca visited during our expeditions for the valuable information provided, their time, and the amazing hospitality. Acknowledgements extended to Pierre Campredon and Ant\u0026oacute;nio Ara\u0026uacute;jo for facilitating crocodile samples and to Miguel Lecoq for providing extensive information on the crocodiles in the Bijagos Islands. Fieldwork was financed by the project TROPIBIO (CIBIO, Vair\u0026atilde;o, Portugal; European Union\u0026apos;s Horizon 2020 research and innovation programme under grant agreement no. 854248). Camera trapping was co-funded by the Elephant Crisis Fund (Save the Elephants/Wildlife Conservation Network) - Projects GW_ICE-01, GW_CIB_02 and 03). CP, JCB, MLL and RG are financed by FCT - Funda\u0026ccedil;\u0026atilde;o para a Ci\u0026ecirc;ncia e Tecnologia (2020.05054.BD, CEECINST/00014/2018/CP1512/CT0001, CEECINSTLA/00020/2022 and 2022.07926. CEECIND, respectively), LP and field missions were supported by national Portuguese funds through FCT - InBIO Program\u0026aacute;tico FUI 2020-2023 (UIDP/50027/2020).\u003c/p\u003e\n\u003cp\u003e\u003cstrong\u003eAuthor contributions\u003c/strong\u003e\u003c/p\u003e\n\u003cp\u003eCP, OR, RG, and JCB conceptualised the study, its methodology and wrote the original draft of the manuscript; CP performed the formal analyses under JCB, OR, and RG supervision; CP, LP, WAI, OR, RG \u0026nbsp;and JCB were gathered data and resources needed for the developing of the applied methodology; CP, LP, WAI, RG, and JCB curated the data; CP, AFP, LP, ML, RG, and JCB acquired the financial support for the project leading to this publication. All the authors contributed to the preparation, creation and presentation of the published work.\u003c/p\u003e\n\u003cp\u003e\u003cstrong\u003eData availability statement\u003c/strong\u003e\u003c/p\u003e\n\u003cp\u003eThe datasets generated and analysed during the current study are available in the Zenodo repository at: https://zenodo.org/records/14975165?preview=1\u0026amp;token=eyJhbGciOiJIUzUxMiJ9.eyJpZCI6ImVkMzdmY2Y4LTI2MGQtNDgzZC1iNzc1LTM4Y2RlNmFiMTE5MCIsImRhdGEiOnt9\u003cbr\u003eLCJyYW5kb20iOiJjYWJjNmZkODFmMWEwOTRjODQ4NWJkZDllZmI2MDdkOCJ9.FM70mJCXkMrMRTbTTlyCL6DlWSLb631k--QDgTInLZdxuO-L_NMhWO8Ua2T-r2jga1nocp8XSpvbgPdoxlvTBw\u003c/p\u003e"},{"header":"References","content":"\u003col\u003e\n\u003cli\u003eAlbert, J. S. \u003cem\u003eet al.\u003c/em\u003e Scientists\u0026rsquo; warning to humanity on the freshwater biodiversity crisis. \u003cem\u003eAmbio\u003c/em\u003e \u003cstrong\u003e50\u003c/strong\u003e, 85\u0026ndash;94 (2021).\u003c/li\u003e\n\u003cli\u003eSayer, C. A. \u003cem\u003eet al.\u003c/em\u003e One-quarter of freshwater fauna threatened with extinction. \u003cem\u003eNature\u003c/em\u003e \u003cstrong\u003e638\u003c/strong\u003e, 138\u0026ndash;145 (2025).\u003c/li\u003e\n\u003cli\u003eFarooq, H., Azevedo, J. A. R., Soares, A., Antonelli, A. \u0026amp; Faurby, S. Mapping Africa\u0026rsquo;s Biodiversity: More of the Same Is Just Not Good Enough. \u003cem\u003eSyst. Biol.\u003c/em\u003e \u003cstrong\u003e70\u003c/strong\u003e, 623\u0026ndash;633 (2021).\u003c/li\u003e\n\u003cli\u003eMyers, N., Mittermeier, R. A., Mittermeier, C. G., Da Fonseca, G. A. B. \u0026amp; Kent, J. Biodiversity hotspots for conservation priorities. \u003cem\u003eNature\u003c/em\u003e \u003cstrong\u003e403\u003c/strong\u003e, 853\u0026ndash;858 (2000).\u003c/li\u003e\n\u003cli\u003eOates, J. F., Bergl, R. A. \u0026amp; Linder, J. M. Africa\u0026rsquo;s Gulf of Guinea Forests: Biodiversity Patterns and Conservation Priorities.\u003c/li\u003e\n\u003cli\u003eBrito, J. C. \u003cem\u003eet al.\u003c/em\u003e Unravelling biodiversity, evolution and threats to conservation in the Sahara‐Sahel. \u003cem\u003eBiol. Rev.\u003c/em\u003e \u003cstrong\u003e89\u003c/strong\u003e, 215\u0026ndash;231 (2014).\u003c/li\u003e\n\u003cli\u003edos Reis-SilvaF., P., A. F. Amphibian and reptile dataset across different land-use types in Guinea-Bissau. (2024) doi:https://doi.org/10.1101/2024.11.21.624282.\u003c/li\u003e\n\u003cli\u003eLuiselli, L. \u003cem\u003eet al.\u003c/em\u003e State of knowledge of research in the Guinean forests of West Africa region. \u003cem\u003eActa Oecologica\u003c/em\u003e \u003cstrong\u003e94\u003c/strong\u003e, 3\u0026ndash;11 (2019).\u003c/li\u003e\n\u003cli\u003eHortal, J. \u003cem\u003eet al.\u003c/em\u003e Seven Shortfalls that Beset Large-Scale Knowledge of Biodiversity. \u003cem\u003eAnnu. Rev. Ecol. Evol. Syst.\u003c/em\u003e \u003cstrong\u003e46\u003c/strong\u003e, 523\u0026ndash;549 (2015).\u003c/li\u003e\n\u003cli\u003eMazzotti, F. J. \u003cem\u003eet al.\u003c/em\u003e Alligators and crocodiles as indicators for restoration of Everglades ecosystems. \u003cem\u003eEcol. Indic.\u003c/em\u003e \u003cstrong\u003e9\u003c/strong\u003e, S137\u0026ndash;S149 (2009).\u003c/li\u003e\n\u003cli\u003eVan Der Ploeg, J., Cauillan-Cureg, M., Van Weerd, M. \u0026amp; Persoon, G. \u0026lsquo;Why must we protect crocodiles?\u0026rsquo; Explaining the value of the Philippine crocodile to rural communities. \u003cem\u003eJ. Integr. Environ. Sci.\u003c/em\u003e \u003cstrong\u003e8\u003c/strong\u003e, 287\u0026ndash;298 (2011).\u003c/li\u003e\n\u003cli\u003eSomaweera, R. \u003cem\u003eet al.\u003c/em\u003e The ecological importance of crocodylians: towards evidence‐based justification for their conservation. \u003cem\u003eBiol. Rev.\u003c/em\u003e \u003cstrong\u003e95\u003c/strong\u003e, 936\u0026ndash;959 (2020).\u003c/li\u003e\n\u003cli\u003eHumphries, M. S., Myburgh, J. G., Campbell, R., Buah-Kwofie, A. \u0026amp; Combrink, X. Organochlorine pesticide bioaccumulation in wild Nile crocodile (Crocodylus niloticus) fat tissues: Environmental influences on changing residue levels and contaminant profiles. \u003cem\u003eSci. Total Environ.\u003c/em\u003e \u003cstrong\u003e753\u003c/strong\u003e, 142068 (2021).\u003c/li\u003e\n\u003cli\u003eRainwater, T. R. \u003cem\u003eet al.\u003c/em\u003e Fauna Associated with American Alligator (Alligator mississippiensis) Nests in Coastal South Carolina, USA. \u003cem\u003eAnimals\u003c/em\u003e \u003cstrong\u003e14\u003c/strong\u003e, 620 (2024).\u003c/li\u003e\n\u003cli\u003eOur\u0026eacute;, R. B. \u0026amp; Sinsin, B. Does Crocodile Conservation Matter in Sacred Natural Sites of Benin (Western Africa)? \u003cem\u003eWest Afr. J. Appl. Ecol.\u003c/em\u003e \u003cstrong\u003e31\u003c/strong\u003e, (2023).\u003c/li\u003e\n\u003cli\u003ePooley, S. A Cultural Herpetology of Nile Crocodiles in Africa. \u003cem\u003eConserv. Soc.\u003c/em\u003e \u003cstrong\u003e14\u003c/strong\u003e, 391\u0026ndash;405 (2016).\u003c/li\u003e\n\u003cli\u003eHekkala, E. \u003cem\u003eet al.\u003c/em\u003e An ancient icon reveals new mysteries: Mummy DNA resurrects a cryptic species within the Nile crocodile. \u003cem\u003eMol. Ecol.\u003c/em\u003e \u003cstrong\u003e20\u003c/strong\u003e, 4199\u0026ndash;4215 (2011).\u003c/li\u003e\n\u003cli\u003eShirley, M. H., Vliet, K. A., Carr, A. N. \u0026amp; Austin, J. D. Rigorous approaches to species delimitation have significant implications for African crocodilian systematics and conservation. \u003cem\u003eProc. R. Soc. B Biol. Sci.\u003c/em\u003e \u003cstrong\u003e281\u003c/strong\u003e, 20132483 (2014).\u003c/li\u003e\n\u003cli\u003eShirley, M. H., Carr, A. N., Nestler, J. H., Vliet, K. A. \u0026amp; Brochu, C. A. Systematic revision of the living African slender-snouted crocodiles (Mecistops gray, 1844). \u003cem\u003eZootaxa\u003c/em\u003e \u003cstrong\u003e4504\u003c/strong\u003e, 151\u0026ndash;193 (2018).\u003c/li\u003e\n\u003cli\u003eVelo-Ant\u0026oacute;n, G., Godinho, R., Campos, J. C. \u0026amp; Brito, J. C. Should i stay or should i go? Dispersal and population structure in small, isolated desert populations of west african crocodiles. \u003cem\u003ePLoS ONE\u003c/em\u003e \u003cstrong\u003e9\u003c/strong\u003e, (2014).\u003c/li\u003e\n\u003cli\u003eCunningham, S. W., Shirley, M. H. \u0026amp; Hekkala, E. R. Fine scale patterns of genetic partitioning in the rediscovered African crocodile, Crocodylus suchus (Saint-Hilaire 1807). \u003cem\u003ePeerJ\u003c/em\u003e \u003cstrong\u003e2016\u003c/strong\u003e, (2016).\u003c/li\u003e\n\u003cli\u003evan Asch, B. \u003cem\u003eet al.\u003c/em\u003e Phylogeography, genetic diversity, and population structure of Nile crocodile populations at the fringes of the southern African distribution. \u003cem\u003ePLoS ONE\u003c/em\u003e \u003cstrong\u003e14\u003c/strong\u003e, (2019).\u003c/li\u003e\n\u003cli\u003eUNEP-WCMC. UNEP-WCMC Species Database: CITES-Listed Species. (2024).\u003c/li\u003e\n\u003cli\u003eLuiselli, L. \u003cem\u003eet al.\u003c/em\u003e Understanding the influence of non-wealth factors in determining bushmeat consumption: Results from four West African countries. \u003cem\u003eActa Oecologica\u003c/em\u003e \u003cstrong\u003e94\u003c/strong\u003e, 47\u0026ndash;56 (2019).\u003c/li\u003e\n\u003cli\u003eShirley, M.H. Mecistops cataphractus: Shirley, M.H.: The IUCN Red List of Threatened Species 2014: e.T5660A3044332. https://doi.org/10.2305/IUCN.UK.2014-1.RLTS.T5660A3044332.en (2013).\u003c/li\u003e\n\u003cli\u003eEaton, M. J., Martin, A., Thorbjarnarson, J. \u0026amp; Amato, G. Species-level diversification of African dwarf crocodiles (Genus Osteolaemus): A geographic and phylogenetic perspective. \u003cem\u003eMol. Phylogenet. Evol.\u003c/em\u003e \u003cstrong\u003e50\u003c/strong\u003e, 496\u0026ndash;506 (2009).\u003c/li\u003e\n\u003cli\u003eTrape, J.-F., Trape, S. \u0026amp; Chirio, L. \u003cem\u003eL\u0026eacute;zards, Crocodiles et Tortues d\u0026rsquo;Afrique Occidentale et Du Sahara\u003c/em\u003e. (IRD \u0026Eacute;ditions, 2012). doi:10.4000/books.irdeditions.37699.\u003c/li\u003e\n\u003cli\u003eSmolensky, N. L., Hurtado, L. A. \u0026amp; Fitzgerald, L. A. DNA barcoding of Cameroon samples enhances our knowledge on the distributional limits of putative species of Osteolaemus (African dwarf crocodiles). \u003cem\u003eConserv. Genet.\u003c/em\u003e \u003cstrong\u003e16\u003c/strong\u003e, 235\u0026ndash;240 (2015).\u003c/li\u003e\n\u003cli\u003eRoss J.P. Crocodiles. Status Survey and Conservation Action Plan. 2nd Edition. IUCN/SSC Crocodile Specialist Group. (1998).\u003c/li\u003e\n\u003cli\u003eNaabeh, C. S. S., Oppong, S. K., Amoah, E., Ahmed, S. \u0026amp; Anokye, A. The Vulnerable West African Dwarf Crocodile (Osteolaemus Sp. Aff. Tetraspis) is Worth Conserving in Urban Ecosystems: Evidence from Ghana. Preprint at https://doi.org/10.21203/rs.3.rs-2778658/v1 (2023).\u003c/li\u003e\n\u003cli\u003eOgorode, O., Vincent-Akpu, F., Babatunde, B., Ijeomah, M. \u0026amp; Olaleru, F. ILLEGAL WILDLIFE TRADE AND OSTEOLAEMU STETRASPIS: A CASE STUDY OF ACTIVITIES IN BUSHMEAT MARKETS UWA AND EDUMANOM IN NIGER DELTA, NIGERIA. (2023).\u003c/li\u003e\n\u003cli\u003eOlunusi, B. O. Wildlife trade dynamics: exploring bushmeat market with a view toward social and ecological justice in Ibadan Metropolis Nigeria. \u003cem\u003eFront. Conserv. Sci.\u003c/em\u003e \u003cstrong\u003e5\u003c/strong\u003e, 1401308 (2024).\u003c/li\u003e\n\u003cli\u003eAuliya, M., Wagner, P. \u0026amp; B\u0026ouml;hme, W. The herpetofauna of the Bijag\u0026oacute;s archipelago, Guinea-Bissau (West Africa) and a first country-wide checklist.\u003c/li\u003e\n\u003cli\u003eGra\u0026ccedil;a L. Fotos \u0026agrave; procura de... uma legenda (153): Uma vez por todas, n\u0026atilde;o havia nem h\u0026aacute; \u0026lsquo;jacar\u0026eacute;s\u0026rsquo; na Guin\u0026eacute;-Bissau, mas \u0026lsquo;crocodilos\u0026rsquo; (e outros r\u0026eacute;pteis). \u003cem\u003eLu\u0026iacute;s Gra\u0026ccedil;a \u0026amp; Camaradas da Guin\u0026eacute;\u003c/em\u003e https://blogueforanadaevaotres.blogspot.com/2021/07/guine-6174-p22399-fotos-procura-de-uma.html.\u003c/li\u003e\n\u003cli\u003eBenoit Limoges \u0026amp; Marie-Jos\u0026eacute;e Robillard. Proposition d\u0026rsquo;un plan d\u0026rsquo;am\u0026eacute;nagement de la r\u0026eacute;serve de la biosph\u0026egrave;re de l\u0026rsquo;archipel des Bijagos. Volume 2. Les esp\u0026egrave;ces. (1991) doi:10.13140/RG.2.2.17554.79044.\u003c/li\u003e\n\u003cli\u003eIUCN. Crocodylus niloticus: Isberg, S., Combrink, X., Lippai, C. \u0026amp; Balaguera-Reina, S.A.: The IUCN Red List of Threatened Species 2019: e.T45433088A3010181. https://doi.org/10.2305/IUCN.UK.2019-1.RLTS.T45433088A3010181.en (2017).\u003c/li\u003e\n\u003cli\u003eSchmitz, A. \u003cem\u003eet al.\u003c/em\u003e Molecular evidence for species level divergence in African Nile Crocodiles Crocodylus niloticus (Laurenti, 1786). \u003cem\u003eComptes Rendus Palevol\u003c/em\u003e \u003cstrong\u003e2\u003c/strong\u003e, 703\u0026ndash;712 (2003).\u003c/li\u003e\n\u003cli\u003eKumi, N. \u0026amp; Abiodun, B. J. Potential impacts of 1.5 \u0026deg;C and 2 \u0026deg;C global warming on rainfall onset, cessation and length of rainy season in West Africa. \u003cem\u003eEnviron. Res. Lett.\u003c/em\u003e \u003cstrong\u003e13\u003c/strong\u003e, 055009 (2018).\u003c/li\u003e\n\u003cli\u003eBarnett, L. K., Emms, C. \u0026amp; Santoni, C. THE HERPETOFAUNA OF ABUKO NATURE RESERVE, THE GAMBIA. (2001).\u003c/li\u003e\n\u003cli\u003eVenter, J. A., Fouch\u0026eacute;, P. S. O. \u0026amp; Vlok, W. Current distribution of the southern barred minnow, Opsaridium peringueyi (Pisces: Cyprinidae), in South Africa: Is there reason for concern? \u003cem\u003eAfr. Zool.\u003c/em\u003e \u003cstrong\u003e45\u003c/strong\u003e, 244\u0026ndash;253 (2010).\u003c/li\u003e\n\u003cli\u003eBrandt, M. \u003cem\u003eet al.\u003c/em\u003e Reduction of tree cover in West African woodlands and promotion in semi-arid farmlands. \u003cem\u003eNat. Geosci.\u003c/em\u003e \u003cstrong\u003e11\u003c/strong\u003e, 328\u0026ndash;333 (2018).\u003c/li\u003e\n\u003cli\u003eHerrmann, S. M., Brandt, M., Rasmussen, K. \u0026amp; Fensholt, R. Accelerating land cover change in West Africa over four decades as population pressure increased. \u003cem\u003eCommun. Earth Environ.\u003c/em\u003e \u003cstrong\u003e1\u003c/strong\u003e, 53 (2020).\u003c/li\u003e\n\u003cli\u003eAyamba, A. J., Thomas, T. K., Ajebe, H. N., Juscar, N. \u0026amp; Venceslas, P. M. Distribution of Dwarf Crocodile (Osteolaemus Tetraspis Cope, 1861) Populations on the Outskirts of the Ebo Forest: Implications for Conservation. \u003cem\u003eAm. J. Environ. Stud.\u003c/em\u003e \u003cstrong\u003e7\u003c/strong\u003e, 1\u0026ndash;14 (2024).\u003c/li\u003e\n\u003cli\u003eFerreira Da Silva, M. J. \u003cem\u003eet al.\u003c/em\u003e Disrupted dispersal and its genetic consequences: Comparing protected and threatened baboon populations (Papio papio) in West Africa. \u003cem\u003ePLOS ONE\u003c/em\u003e \u003cstrong\u003e13\u003c/strong\u003e, e0194189 (2018).\u003c/li\u003e\n\u003cli\u003eBecker, M. S. \u003cem\u003eet al.\u003c/em\u003e Wire-snare bushmeat poaching and the large African carnivore guild: Impacts, knowledge gaps, and field-based mitigation. \u003cem\u003eBiol. Conserv.\u003c/em\u003e \u003cstrong\u003e289\u003c/strong\u003e, 110376 (2024).\u003c/li\u003e\n\u003cli\u003eWegner, G. I. \u003cem\u003eet al.\u003c/em\u003e Averting wildlife-borne infectious disease epidemics requires a focus on socio-ecological drivers and a redesign of the global food system. \u003cem\u003eeClinicalMedicine\u003c/em\u003e \u003cstrong\u003e47\u003c/strong\u003e, 101386 (2022).\u003c/li\u003e\n\u003cli\u003ePublic health risks involved in the human consumption of reptile meat - Scientific Opinion of the Panel on Biological Hazards. \u003cem\u003eEFSA J.\u003c/em\u003e doi:10.2903/j.efsa.2007.578.\u003c/li\u003e\n\u003cli\u003eAbrahms, B. \u003cem\u003eet al.\u003c/em\u003e Climate change as a global amplifier of human\u0026ndash;wildlife conflict. \u003cem\u003eNat. Clim. Change\u003c/em\u003e \u003cstrong\u003e13\u003c/strong\u003e, 224\u0026ndash;234 (2023).\u003c/li\u003e\n\u003cli\u003eMekonen, S. Coexistence between human and wildlife: the nature, causes and mitigations of human wildlife conflict around Bale Mountains National Park, Southeast Ethiopia. \u003cem\u003eBMC Ecol.\u003c/em\u003e \u003cstrong\u003e20\u003c/strong\u003e, 51 (2020).\u003c/li\u003e\n\u003cli\u003eChakanyuka, T. \u0026amp; Utete, B. Adaptive co‐management, co‐existence or just wildlife conservation? Case study of the human and Nile crocodile ( \u003cem\u003eCrocodylus niloticus\u003c/em\u003e ) conflicts in Ngezi Dam, Mashonaland West, Zimbabwe. \u003cem\u003eAfr. J. Ecol.\u003c/em\u003e \u003cstrong\u003e60\u003c/strong\u003e, 759\u0026ndash;768 (2022).\u003c/li\u003e\n\u003cli\u003eAshepet, M.-G., Dahdouh-Guebas, F., Redpath, S., Pooley, S. \u0026amp; Huge, J. The state and perceptions of human-crocodile interactions around Murchison falls conservation area, Uganda. \u003cem\u003eHum. Dimens. Wildl.\u003c/em\u003e \u003cstrong\u003e29\u003c/strong\u003e, 194\u0026ndash;209 (2024).\u003c/li\u003e\n\u003cli\u003eWorld Bank. Guinea-Bissau: Development news, research, data. World Development Indicators. https://data.worldbank.org/country/guinea-bissau. https://data.worldbank.org/country/guinea-bissau.\u003c/li\u003e\n\u003cli\u003eRaimundo Lopes, N. D., Li, T., Qian, D., Matomela, N. \u0026amp; S\u0026aacute;, R. M. Factors influencing coastal land cover change and corresponding impact on habitat quality in the North-western Coastline of Guinea-Bissau (NC-GB). \u003cem\u003eOcean Coast. Manag.\u003c/em\u003e \u003cstrong\u003e224\u003c/strong\u003e, 106181 (2022).\u003c/li\u003e\n\u003cli\u003eTemudo, M. P. \u0026amp; Santos, P. Shifting environments in Eastern Guinea-Bissau, West Africa: The length of fallows in question. \u003cem\u003eNJAS Wagening. J. Life Sci.\u003c/em\u003e \u003cstrong\u003e80\u003c/strong\u003e, 57\u0026ndash;64 (2017).\u003c/li\u003e\n\u003cli\u003eAmoah, E., Danquah, E. \u0026amp; Perran Ross, J. Nesting Ecology of West African Dwarf Crocodiles in a Heavily Disturbed Landscape in Chirehin, Ghana. \u003cem\u003eInt. J. Ecol.\u003c/em\u003e \u003cstrong\u003e2021\u003c/strong\u003e, 1\u0026ndash;11 (2021).\u003c/li\u003e\n\u003cli\u003eCampos, J. C., Mart\u0026iacute;nez-Freir\u0026iacute;a, F., Sousa, F. V., Santar\u0026eacute;m, F. \u0026amp; Brito, J. C. Update of distribution, habitats, population size, and threat factors for the West African crocodile in Mauritania. \u003cem\u003eAmphib. Reptil.\u003c/em\u003e \u003cstrong\u003e37\u003c/strong\u003e, 325\u0026ndash;330 (2016).\u003c/li\u003e\n\u003cli\u003eMatangi, D. Understanding Human-wildlife conflict and its impact on agroecology transition In Zimbabwe. \u003cem\u003eTech. Rep.\u003c/em\u003e\u003c/li\u003e\n\u003cli\u003eLiu, C., Hu, Y., Taukenova, A., Tian, G. \u0026amp; Mu, B. Identification of Wetland Conservation Gaps in Rapidly Urbanizing Areas: A Case Study in Zhengzhou, China. \u003cem\u003eLand\u003c/em\u003e \u003cstrong\u003e12\u003c/strong\u003e, (2023).\u003c/li\u003e\n\u003cli\u003eKp\u0026eacute;ra, G. N. \u003cem\u003eet al.\u003c/em\u003e \u0026lsquo;A pond with crocodiles never dries up\u0026rsquo;: a frame analysis of human\u0026ndash;crocodile relationships in agro-pastoral dams in Northern Benin. \u003cem\u003eInt. J. Agric. Sustain.\u003c/em\u003e \u003cstrong\u003e12\u003c/strong\u003e, 316\u0026ndash;333 (2014).\u003c/li\u003e\n\u003cli\u003ePalmeirim, A. F., Seck, S., Palma, L. \u0026amp; Ladle, R. J. Shifting values and the fate of sacred forests in Guinea-Bissau: are community-managed forests the answer? \u003cem\u003eEnviron. Conserv.\u003c/em\u003e \u003cstrong\u003e50\u003c/strong\u003e, 152\u0026ndash;155 (2023).\u003c/li\u003e\n\u003cli\u003ePalma, L. \u003cem\u003eet al.\u003c/em\u003e African Forest elephants persist in Guinea-Bissau but require an emergency conservation plan. \u003cem\u003eOryx\u003c/em\u003e \u003cstrong\u003e58\u003c/strong\u003e, 125\u0026ndash;128 (2024).\u003c/li\u003e\n\u003cli\u003eIUCN. Unified Classification of Direct Threats Version 3.3. (2022).\u003c/li\u003e\n\u003cli\u003eBoom, R. \u003cem\u003eet al.\u003c/em\u003e Rapid and simple method for purification of nucleic acids. \u003cem\u003eJ. Clin. Microbiol.\u003c/em\u003e \u003cstrong\u003e28\u003c/strong\u003e, 495\u0026ndash;503 (1990).\u003c/li\u003e\n\u003cli\u003eJanke, A. \u0026amp; Arnason, U. The complete mitochondrial genome of Alligator mississippiensis and the separation between recent archosauria (birds and crocodiles). \u003cem\u003eMol. Biol. Evol.\u003c/em\u003e \u003cstrong\u003e14\u003c/strong\u003e, 1266\u0026ndash;1272 (1997).\u003c/li\u003e\n\u003cli\u003eFranke, F. A. \u003cem\u003eet al.\u003c/em\u003e Genetic differentiation of the African dwarf crocodile Osteolaemus tetraspis Cope, 1861 (Crocodylia: Crocodylidae) and consequences for European zoos. \u003cem\u003eOrg. Divers. Evol.\u003c/em\u003e \u003cstrong\u003e13\u003c/strong\u003e, 255\u0026ndash;266 (2013).\u003c/li\u003e\n\u003cli\u003eHekkala, E. R. \u003cem\u003eet al.\u003c/em\u003e The secrets of Sobek \u0026ndash; A crocodile mummy mitogenome from ancient Egypt. \u003cem\u003eJ. Archaeol. Sci. Rep.\u003c/em\u003e \u003cstrong\u003e33\u003c/strong\u003e, (2020).\u003c/li\u003e\n\u003cli\u003eBouckaert, R. \u003cem\u003eet al.\u003c/em\u003e BEAST 2.5: An advanced software platform for Bayesian evolutionary analysis. \u003cem\u003ePLOS Comput. Biol.\u003c/em\u003e \u003cstrong\u003e15\u003c/strong\u003e, e1006650 (2019).\u003c/li\u003e\n\u003cli\u003eMinh, B. Q. \u003cem\u003eet al.\u003c/em\u003e IQ-TREE 2: New Models and Efficient Methods for Phylogenetic Inference in the Genomic Era. \u003cem\u003eMol. Biol. Evol.\u003c/em\u003e \u003cstrong\u003e37\u003c/strong\u003e, 1530\u0026ndash;1534 (2020).\u003c/li\u003e\n\u003cli\u003eRambaut, A., Drummond, A. J., Xie, D., Baele, G. \u0026amp; Suchard, M. A. Posterior Summarization in Bayesian Phylogenetics Using Tracer 1.7. \u003cem\u003eSyst. Biol.\u003c/em\u003e \u003cstrong\u003e67\u003c/strong\u003e, 901\u0026ndash;904 (2018).\u003c/li\u003e\n\u003c/ol\u003e"}],"fulltextSource":"","fullText":"","funders":[],"hasAdminPriorityOnWorkflow":false,"hasManuscriptDocX":true,"hasOptedInToPreprint":true,"hasPassedJournalQc":"","hasAnyPriority":false,"hideJournal":false,"highlight":"","institution":"","isAcceptedByJournal":true,"isAuthorSuppliedPdf":false,"isDeskRejected":"","isHiddenFromSearch":false,"isInQc":false,"isInWorkflow":false,"isPdf":false,"isPdfUpToDate":true,"isWithdrawnOrRetracted":false,"journal":{"display":true,"email":"[email protected]","identity":"scientific-reports","isNatureJournal":false,"hasQc":true,"allowDirectSubmit":false,"externalIdentity":"scirep","sideBox":"Learn more about [Scientific Reports](http://www.nature.com/srep/)","snPcode":"","submissionUrl":"","title":"Scientific Reports","twitterHandle":"","acdcEnabled":true,"dfaEnabled":true,"editorialSystem":"stoa","reportingPortfolio":"Scientific Reports","inReviewEnabled":true,"inReviewRevisionsEnabled":true},"keywords":"West Africa, non-invasive genetic, habitat degradation, human-wildlife conflict, freshwater biodiversity, Crocodylus niloticus","lastPublishedDoi":"10.21203/rs.3.rs-6183800/v1","lastPublishedDoiUrl":"https://doi.org/10.21203/rs.3.rs-6183800/v1","license":{"name":"CC BY 4.0","url":"https://creativecommons.org/licenses/by/4.0/"},"manuscriptAbstract":"\u003cp\u003eChallenges in freshwater organism conservation in West Africa are worsened by significant knowledge gaps, even for charismatic species like crocodiles. This study addresses these gaps by assessing crocodile diversity, distribution, and conservation threats in Guinea-Bissau, where existing data is outdated. We used visual surveys, inquiries, molecular barcoding, camera trapping, and bibliographic reviews to investigate crocodile populations. Notably, we found evidence suggesting the Nile crocodile (\u003cem\u003eCrocodylus niloticus\u003c/em\u003e), previously thought extinct in West Africa since about 200 years, may persist in the Cacheu region (Guinea-Bissau). We also confirmed the presence of the West African crocodile (\u003cem\u003eCrocodylus suchus\u003c/em\u003e) in major river basins and coastal lagoons, including the Bijag\u0026oacute;s Archipelago, and the West African dwarf crocodile (\u003cem\u003eOsteolaemus cf tetraspis\u003c/em\u003e) in the southern mainland and the Bijag\u0026oacute;s Archipelago. Habitat loss and deliberate killings were identified as major threats. Standardized surveys and genetic sampling are essential to assess population size, connectivity, and genetic diversity, informing evolutionary studies and conservation planning. Conservation efforts should prioritize habitat protection through community-managed reserves and restoration initiatives. Additionally, engaging local communities to raise awareness and develop conflict mitigation strategies is crucial, particularly in areas with human-crocodile interactions.\u003c/p\u003e","manuscriptTitle":"Diversity, distribution and conservation of crocodiles (Order: Crocodylia) in Guinea-Bissau, West Africa","msid":"","msnumber":"","nonDraftVersions":[{"code":1,"date":"2025-03-31 06:27:49","doi":"10.21203/rs.3.rs-6183800/v1","editorialEvents":[{"type":"communityComments","content":0},{"type":"decision","content":"Revision requested","date":"2025-04-14T05:10:46+00:00","index":"","fulltext":""},{"type":"editorInvitedReview","content":"","date":"2025-04-12T18:09:07+00:00","index":"hide","fulltext":""},{"type":"editorInvitedReview","content":"","date":"2025-04-12T01:39:48+00:00","index":"hide","fulltext":""},{"type":"reviewerAgreed","content":"17003959953121217059571576329358917877","date":"2025-03-23T21:21:43+00:00","index":"hide","fulltext":""},{"type":"reviewerAgreed","content":"74424956800143436720946536529092595980","date":"2025-03-22T06:33:58+00:00","index":"hide","fulltext":""},{"type":"reviewersInvited","content":"","date":"2025-03-21T19:26:06+00:00","index":"","fulltext":""},{"type":"editorAssigned","content":"","date":"2025-03-21T19:02:55+00:00","index":"","fulltext":""},{"type":"editorInvited","content":"","date":"2025-03-21T05:18:05+00:00","index":"","fulltext":""},{"type":"checksComplete","content":"","date":"2025-03-20T04:35:21+00:00","index":"","fulltext":""},{"type":"submitted","content":"Scientific Reports","date":"2025-03-08T11:12:11+00:00","index":"","fulltext":""}],"status":"published","journal":{"display":true,"email":"[email protected]","identity":"scientific-reports","isNatureJournal":false,"hasQc":true,"allowDirectSubmit":false,"externalIdentity":"scirep","sideBox":"Learn more about [Scientific Reports](http://www.nature.com/srep/)","snPcode":"","submissionUrl":"","title":"Scientific Reports","twitterHandle":"","acdcEnabled":true,"dfaEnabled":true,"editorialSystem":"stoa","reportingPortfolio":"Scientific Reports","inReviewEnabled":true,"inReviewRevisionsEnabled":true}}],"origin":"","ownerIdentity":"4681cae8-db69-4442-a1f6-2a5be61ebf40","owner":[],"postedDate":"March 31st, 2025","published":true,"recentEditorialEvents":[],"rejectedJournal":[],"revision":"","amendment":"","status":"published-in-journal","subjectAreas":[{"id":46223786,"name":"Biological sciences/Ecology/Biodiversity"},{"id":46223787,"name":"Biological sciences/Evolution/Taxonomy"},{"id":46223788,"name":"Biological sciences/Zoology/Herpetology"},{"id":46223789,"name":"Earth and environmental sciences/Ecology/Biodiversity"},{"id":46223790,"name":"Earth and environmental sciences/Ecology/Biogeography"},{"id":46223791,"name":"Earth and environmental sciences/Ecology/Conservation"},{"id":46223792,"name":"Earth and environmental sciences/Ecology/Freshwater ecology"}],"tags":[],"updatedAt":"2025-07-14T16:02:52+00:00","versionOfRecord":{"articleIdentity":"rs-6183800","link":"https://doi.org/10.1038/s41598-025-08789-3","journal":{"identity":"scientific-reports","isVorOnly":false,"title":"Scientific Reports"},"publishedOn":"2025-07-09 15:57:45","publishedOnDateReadable":"July 9th, 2025"},"versionCreatedAt":"2025-03-31 06:27:49","video":"","vorDoi":"10.1038/s41598-025-08789-3","vorDoiUrl":"https://doi.org/10.1038/s41598-025-08789-3","workflowStages":[]},"version":"v1","identity":"rs-6183800","journalConfig":"researchsquare"},"__N_SSP":true},"page":"/article/[identity]/[[...version]]","query":{"redirect":"/article/rs-6183800","identity":"rs-6183800","version":["v1"]},"buildId":"8U1c8b4HqxoKbykW_rLl7","isFallback":false,"isExperimentalCompile":false,"dynamicIds":[84888],"gssp":true,"scriptLoader":[]}