Comparative Phylogeography of Central African Duikers Using Non-invasive Sampling Methods

The present study sets out to assess patterns of evolutionary diversification in central African duikers (subfamily Cephalophinae). The sampling strategy consisted of collecting geo-referenced duiker feces across 43 sites and seven countries. However, several challenges related to the use of non-invasive samples needed to be addressed prior to large scale DNA amplification. First, the best storage method for obtaining DNA from fecal samples needed to be established. Our study revealed that while silica is best for nuclear microsatellite analyses, RNAlater is the best storage medium for maximal mitochondrial amplification. Moreover, extracting DNA as early as possible always provided the best results. Second, since it is impossible to determine the species identity of duiker feces solely based on their morphology, a simple and reliable molecular method was needed. A tree-based approach based on ~650 base pairs of the control region amplified from reference samples was found to be the most reliable method to recover the identity of unknown samples. Third, for fine scale analyses of population genetic structure, a set of twelve nuclear microsatellites were assembled from existing bovid data. These microsatellites markers were chosen because they are very polymorphic, cross amplify among targeted taxa, co-amplify with combined markers of the same multiplex, and are powerful enough for individual identification. Patterns of mitochondrial and nuclear microsatellite variation were used to test two important hypotheses of diversification in the tropics: the Pleistocene refugia and the riverine barrier hypotheses. Analyses of historical and contemporary population genetic structure were carried out on the three most abundant species in our sampling area: the bay duiker (C. dorsalis), the Peter’s duiker (C. callipygus), and the blue duiker (P. monticola) using mitochondrial and nuclear markers described above. These data show that (1) southwest Nigeria and southwest Cameroon comprise genetically distinct populations in C. callipygus and P. monticola species, (2) signatures of demographic expansion for all three taxa are broadly coincident with the location of hypothesized upland refugia in Gabon and Equatorial Guinea and (3) the Sanaga, Ogooué, and Sangha rivers may constitute a partial riverine barrier and/or act as fluvial refugia for duikers

Environmental variation predicts patterns of genomic variation in an African tropical forest frog

Central African rainforests are predicted to be disproportionately affected by future climate change. How species will cope with these changes is unclear, but rapid environmental changes will likely impose strong selection pressures. Here we examined environmental drivers of genomic variation in the central African puddle frog (Phrynobatrachus auritus) to identify areas of elevated environmentally-associated turnover. We also compared current and future climate models to pinpoint areas of high genomic vulnerability where allele frequencies will have to shift the most in order to keep pace with future climate change. Neither physical landscape barriers nor the effects of past Pleistocene refugia influenced genomic differentiation. Alternatively, geographic distance and seasonal aspects of precipitation are the most important drivers of SNP allele frequency variation. Patterns of genomic differentiation coincided with key ecological gradients across the forest-savanna ecotone, montane areas, and a coastal to interior rainfall gradient. Areas of greatest vulnerability were found in the lower Sanaga basin, the southeastern region of Cameroon, and southwest Gabon. In contrast with past conservation efforts that have focused on hotspots of species richness or endemism, our findings highlight the importance of maintaining environmentally heterogeneous landscapes to preserve genomic variation and ongoing evolutionary processes in the face of climate change

Global forest management data for 2015 at a 100 m resolution

Spatially explicit information on forest management at a global scale is critical for understanding the status of forests, for planning sustainable forest management and restoration, and conservation activities. Here, we produce the first reference data set and a prototype of a globally consistent forest management map with high spatial detail on the most prevalent forest management classes such as intact forests, managed forests with natural regeneration, planted forests, plantation forest (rotation up to 15 years), oil palm plantations, and agroforestry. We developed the reference dataset of 226 K unique locations through a series of expert and crowdsourcing campaigns using Geo-Wiki (https://www.geo-wiki.org/). We then combined the reference samples with time series from PROBA-V satellite imagery to create a global wall-to-wall map of forest management at a 100 m resolution for the year 2015, with forest management class accuracies ranging from 58% to 80%. The reference data set and the map present the status of forest ecosystems and can be used for investigating the value of forests for species, ecosystems and their services

Tourisme d’observation et éléphants de forêt (Loxodonta cyclotis) au Campement de Nyonié, Gabon

Central African ecosystems are home to a rich biodiversity, including the endangered forest elephant (Loxodonta cyclotis). Ecotourism is a growing industry in the region, but it can have a negative impact on elephant populations. This study investigates the relationship between ecotourism and forest elephants at the "Campement de Nyonié" in Gabon, a tourist site located outside of protected areas. Data was collected through direct observations of elephants on foot and in off-road vehicle. Results showed that elephants are present in a large and continuous area around the camp. Their activity is concentrated in the south, near the Wonga-Wongué Presidential Reserve, and in the west, near the coast. Elephants live in matriarchal groups, led by older females. The results suggest that tourist activity at the "Campement de Nyonié" does not drive elephants away. On the contrary, it could even contribute to their conservation by raising public awareness and generating revenue for environmental protection. The study highlights the importance of cooperation between tourism stakeholders and authorities to balance biodiversity conservation and economic development. Keywords: Sighting tourism, Loxodonta cyclotis, spatial distribution, social structuring, Campement de NyoniéLes écosystèmes d'Afrique centrale abritent une importante biodiversité, dont l'éléphant de forêt (Loxodonta cyclotis), une espèce menacée. Le tourisme d'observation de la faune est une activité en plein essor dans la sous-région, mais il peut avoir un impact négatif sur les populations d'éléphants. Une étude a été menée au Campement de Nyonié, au Gabon, un site touristique situé en dehors des aires protégées. Les données ont été collectées par observations directes des éléphants à pied et en voiture tout-terrain. Les résultats montrent que les éléphants sont présents dans une zone large et continue autour du Campement de Nyonié. Leur activité se concentre au sud, près de la Réserve présidentielle de Wonga-Wongué et à l'ouest, près de la côte. Les éléphants vivent en groupes matriarcaux, dirigés par des femelles âgées. Les résultats suggèrent que l'activité touristique du Campement de Nyonié n'éloigne pas les éléphants. Au contraire, elle pourrait même contribuer à leur conservation en favorisant la sensibilisation du public et en générant des revenus pour la protection de l'environnement. Les résultats de cette étude soulignent l'importance de la coopération entre les acteurs du tourisme et les autorités pour concilier la conservation de la biodiversité et le développement économique. Mots clés: Tourisme d’observation, Loxodonta cyclotis, distribution spatiale, structuration sociale, Campement de Nyoni

Rodent malaria in Gabon: Diversity and host range

International audienceMalaria parasites infect a wide range of vertebrate hosts, such as reptiles, birds and mammals (i.e., primates, ungulates, bats, and rodents). Four Plasmodium species and their subspecies infect African Muridae. Since their discoveries in the 1940s, these rodent Plasmodium species have served as biological models to explore many aspects of the biology of malaria agents and their interactions with their hosts. Despite that, surprisingly, little is known about their ecology, natural history and evolution. Most field studies on these parasites, performed from the 1940s to the early 1980s, showed that all rodent Plasmodium species infect only one main host species, the thicket rat. In the present study, we re-explored the diversity of Plasmodium parasites infecting rodent species living in peridomestic habitats in Gabon, Central Africa. Using molecular approaches, we found that at least two Plasmodium species (Plasmodium vinckei and Plasmodium yoelii) circulated among five rodent species (including the invasive species Mus musculus). This suggests that the host range of these parasites might be larger than previously considered. Our results also showed that the diversity of these parasites could be higher than currently recognized, with the discovery of a new phylogenetic lineage that could represent a new species of rodent Plasmodium

Estimation of the census (Nc) and effective (Ne) population size of a wild mandrill (Mandrillus sphinx) horde in the Lopé National Park, Gabon using a non-invasive genetic approach

Mandrills (Mandrillus sphinx) are enigmatic primates endemic to central Africa and are threatened by habitat loss and hunting. However, effective management of this species is limited by insufficient information about their numbers in the wild, since population size can impact viability and genetic diversity. Here, we used for the first time a non-invasive genetic approach to estimate the census and effective population size (Nc and Ne respectively) of a wild mandrill horde in Lopé National Park (Gabon). We amplified a total of 232 unique genotypes using a panel of 16 microsatellite loci from mandrill fecal samples collected over three years (2016–2018). Using the single sample estimator in CAPWIRE, we obtained an estimate for Nc of 989 (95% CI 947–1399) individuals which was close to that obtained from the multiple sample estimator implemented in the program MARK [992 (95% CI 708–1453)]. These estimates approximately correspond with previous visual counts obtained from the same horde. Based on a model implemented in the program NeOGen, when samples were pooled across all three sampling sessions, statistical power was sufficient for a robust Ne estimate. Using the three one-sample estimators in the NeESTIMATORV2 program and the one in COLONY, Ne was estimated at 292 (95% CI 239–370) and 135 (95% CI 108–176) individuals respectively, indicating that Ne is between 13.6 and 29.5% of Nc. This study showed that non-invasive genetics is an effective tool for providing accurate estimates of horde sizes of mandrills and other elusive primates, provided enough samples and hypervariable loci are genotyped.Output Status: Forthcoming/Available Onlin

Caractérisation de la pêche à la senne de plage dans la Réserve Aquatique de Mandji-Etimboué (Gabon)

The conservation of marine biodiversity and the establishment of aquatic protected areas have become a global challenge. Thus, the  continued use of non-selective fishing gear requires a comprehensive and ongoing assessment. With this in mind, the catch rates and  socio-economic aspects of beach seine fishing in the MandjiEtimboué Aquatic Reserve (AR) were examined using landing monitoring as a  methodological approach. The results showed that the average catch per unit effort (CPUE) of beach purse seiners is 393.29 kg/seine  haul. Comparative analysis between CPUE in 2017 and 2021 showed a decrease of 490.9 kg/fishing trip in the rainy season and an  increase of 5.08 kg of fish/fishing trip in the dry season. The decrease in fishing effort and increase in CPUE in this Mandji-Etimboué  beach seine fishery has shown that fishery resources in the Mandji-Etimboué RA are in good health. However, close collaboration  between local communities and administrations is needed. La conservation de la biodiversité marine et la mise en place des aires protégées aquatiques sont devenues un challenge planétaire.  Ainsi, l'utilisation continue d’engins de pêche non sélectifs nécessite une évaluation complète et continue. Dans cette optique, les taux de  capture et les aspects socio-économiques de la pêche à la senne de plage dans la Réserve Aquatique (RA) de Mandji-Etimboué ont été  examinés en utilisant un suivi de débarquement comme approche méthodologique. Les résultats ont montré que les prises par unité  d'effort moyenne (CPUE) des senneurs de plage est de 393,29 kg/coup de senne. L’analyse comparative entre les CPUE de 2017 et  2021 a montré une diminution de 490,9 kg/sortie de pêche en saison des pluies et une augmentation de 5.08 kg de poissons/sortie de  pêche en saison sèche. La diminution de l’effort de pêche et la hausse du CPUE dans cette pêcherie de la senne de plage de Mandji- Etimboué a montré que les ressources halieutiques dans la RA de Mandji-Etimboué sont en bonne santé. Mais, un travail étroit entre les  communautés locales et les administrations doit être mis en place

Preliminary assessment of gastrointestinal parasites of the sun-tailed monkey (Allochrocebus solatus) in a semi-free-ranging colony

Background: The occurrence of gastrointestinal parasites in the sun-tailed monkey (Allochrocebus solatus) at the CIRMF primatology center is unknown. We, therefore, assessed the presence and richness (number of different parasite taxa) of gastrointestinal parasites in a semi-free-ranging colony of A. solatus. Methods: A total of 46 fecal samples were screened using a modified McMaster technique for fecal egg counts. Results: In the 46 samples collected, seven taxa of gastrointestinal parasites, including protozoa and nematodes were identified. The most prevalent parasite was strongyles parasites (98%), followed by Trichuris spp. (72%), Strongyloides spp. (67%) and Entamoeba coli (65%). Balantioides coli (33%), Endolimax nana (25%), and Spirurid eggs (26%) were only found in a minority of the animals. Conclusions: This study contributes new host records of gastrointestinal parasites in semi-free-ranging A. solatus and highlights the need to investigate the health of this species and implement proper precautions in the management of this colony

What mandrills leave behind: using fecal samples to characterize the major histocompatibility complex in a threatened primate

The major histocompatibility complex (MHC) can be useful in guiding conservation planning because of its influence on immunity, fitness, and reproductive ecology in vertebrates. The mandrill (Mandrillus sphinx) is a threatened primate endemic to central Africa. Considerable research in this species has shown that the MHC is important for disease resistance, mate choice, and reproductive success. However, all previous MHC research in mandrills has focused on an inbred semi-captive population, so their genetic diversity may have been underestimated. Here we expand our current knowledge of mandrill MHC variation by performing next-generation sequencing of non-invasively collected fecal samples from a large wild horde in central Gabon. We observe MHC lineages and alleles shared with other primates, and we uncover 45 putative new class II MHC DRB alleles, including representatives of the DRB9 pseudogene, which has not previously been identified in mandrills. We also document methodological challenges associated with fecal samples in NGS-based MHC research. Even with high read depth, the replicability of alleles from fecal samples was lower than that of tissue samples, and allele assignments are inconsistent between sample types. Further, the common assumption that variants with very high read depth should represent true alleles does not appear to be reliable for fecal samples. Nevertheless, the use of degraded DNA in the present study still enabled significant progress in quantifying immunogenetic diversity and its evolution in wild primates

What mandrills leave behind: using fecal samples to characterize the major histocompatibility complex in a threatened primate

The major histocompatibility complex (MHC) can be useful in guiding conservation planning because of its influence on immunity, fitness, and reproductive ecology in vertebrates. The mandrill (Mandrillus sphinx) is a threatened primate endemic to central Africa. Considerable research in this species has shown that the MHC is important for disease resistance, mate choice, and reproductive success. However, all previous MHC research in mandrills has focused on an inbred semi-captive population, so their genetic diversity may have been underestimated. Here we expand our current knowledge of mandrill MHC variation by performing next-generation sequencing of non-invasively collected fecal samples from a large wild horde in central Gabon. We observe MHC lineages and alleles shared with other primates, and we uncover 45 putative new class II MHC DRB alleles, including representatives of the DRB9 pseudogene, which has not previously been identified in mandrills. We also document methodological challenges associated with fecal samples in NGS-based MHC research. Even with high read depth, the replicability of alleles from fecal samples was lower than that of tissue samples, and allele assignments are inconsistent between sample types. Further, the common assumption that variants with very high read depth should represent true alleles does not appear to be reliable for fecal samples. Nevertheless, the use of degraded DNA in the present study still enabled significant progress in quantifying immunogenetic diversity and its evolution in wild primates