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ABSTRACT The western chimpanzee (Pan troglodytes verus) is a Critically Endangered taxon. In Guinea‐Bissau (GB), the subspecies is increasingly threatened, but there is a lack of understanding regarding the degree of genetic threat faced by populations. This hinders the development of targeted conservation strategies and the prioritization of efforts by national agencies. In this study, we use microsatellite data from four parks located in southern GB and five whole‐genome sequences to estimate the effective population size (Ne) and infer the recent and ancient demographic history of populations using different methods. We also aim to integrate the different Ne estimates to improve our understanding of the evolutionary history and current demography of this great ape and to discuss the strengths and limitations of each estimator and their complementarity in informing conservation decisions. Results from the PSMC method suggest a large ancestral Ne, likely due to ancient structure over the whole subspecies distribution until approximately 10,000–15,000 years ago. After that, a change in connectivity, a real decrease in size, or a combination of both occurred, which reduced the then still large ancestral population to a smaller size (MSVAR: ~10,000 decreasing to 1,000–6,000 breeding individuals), possibly indicating a fragmentation into coastal and inland subpopulations. In the most recent past, contemporary Ne is close to 500 (GONE: 395–583, NeEstimator: 107–549), suggesting a high risk of extinction. The populations located at the coastal parks may have been small or isolated for several generations and are at higher risk, whereas the ones located inland exhibit higher long‐term Ne and can be considered a stronghold for chimpanzee conservation. Through combining different types of molecular markers and analytical methodologies, we tried to overcome the limitations of obtaining high‐quality DNA samples from wild threatened populations and estimated Ne at different temporal and spatial scales, which is crucial information to make informed conservation decisions at local and regional scales.

Critically endangered Hooded Vultures ( Necrosyrtes monachus Temminck, 1823), like many vulture species globally, are experiencing rapid population declines due to anthropogenic factors such as poisonings, human persecution, trading for belief-based use, and habitat loss/degradation. The Hooded Vulture is widespread across sub-Saharan Africa. Although it is considered one of the most abundant vultures in West Africa, this vulture species is less common in East and southern Africa, with the population at the southern-most edge of the distribution (in South Africa and Eswatini) estimated at only 100–200 mature individuals. The distribution of Hooded Vultures has contracted dramatically in southern Africa, with breeding populations largely confined to protected areas such as the Greater Kruger National Park. This study aimed to investigate the genetic diversity of the southern African range-edge population and assess if the recent contraction in the distribution has resulted in the population experiencing a genetic bottleneck. Sixteen microsatellite loci were amplified for samples collected along the Olifants River in the Greater Kruger National Park (n = 30). The genetic diversity in the South African population was compared to samples (n = 30) collected in Ghana, where Hooded Vultures are more abundant. Contrary to expectations, the South African peripheral Hooded Vulture population showed higher levels of heterozygosity (H O  = 0.495) than the Ghanaian population (H O  = 0.315). Neither population showed signs of recent bottleneck events when tested using demographic modelling and Approximate Bayesian computation (ABC). However, both populations showed high levels of inbreeding and relatedness. Our results suggest that despite being a small peripheral population, the South African Hooded Vulture population showed a similar level of genetic diversity as individuals sampled from a core population within the species distribution (in Ghana). This study supports the need for Hooded Vulture conservation efforts in the southern African region and highlights the evolutionary importance of range-edge populations.

The West-African sooty mangabey (Cercocebus atys) is threatened by habitat loss, hunting for meat consumption, and mortality during crop-foraging events. The species’ overall demographic trend is unknown. Presence and distribution in Guinea-Bissau, a country neighbored by Senegal and Republic of Guinea, was confirmed in 1946 but the species was declared extinct in 1989 and not observed in subsequent countrywide expeditions. Narratives of its presence across southern Guinea-Bissau are scattered in reports and occurrence in the eastern part was reported in 2017, but the limits of its distribution are currently unknown. Here, we present recent geo-referenced visual and molecular-based records of the sooty mangabey for three protected areas in southern Guinea-Bissau collected as part of a region-wide survey. Individuals were observed in Cufada Lagoons Natural Park (2015) and Dulombi National Park (NP) (2016) and photographed in Boé NP (2007, 2015 and 2020). Thirty-six samples collected in Boé NP (2017) were identified as sooty mangabey using a 402 base pair fragment of the mitochondrial cytochrome b gene. Our work suggests a wider distribution in Guinea-Bissau than previously described, augments knowledge of the populations’ current habitat use and threats, and has implications for efforts to conserve the species in West Africa. Considering the sooty mangabey as the reservoir of the simian immunodeficiency virus that led to the human variant, HIV-2, confirmation that the Guinea-Bissau population is not extinct may lead to a better understanding of early viral jump to humans and consequent epidemic spread, specifically of the HIV-2 Subgroup A. We highlight the need for extra conservation measures by Guinea-Bissau authorities.

The lesser spot-nosed monkey (Cercopithecus petaurista) is a widely distributed West African guenon, which is generally considered less vulnerable to local extinctions than many sympatric primate species. Guinea-Bissau harbours the westernmost populations of the species, which is thought to be very rare or even extinct on the mainland, but to have putative populations on some islands of the Bijagós Archipelago. However, due to a lack of regional studies, baseline information on these insular populations is missing. We collected baseline data on the anthropogenic activities that possibly threaten the long-term conservation of this primate by using non-systematic ethnographic methodologies. The species was reported to be decreasing in number or rare by locals on two of the islands, and we identified two main conservation threats to it: generalised habitat loss/degradation, and hunting. While subsistence hunting has been recorded before in these areas, we report, to the best of our knowledge for the first time for these islands, the presence of a semi-organised commercial wild meat trade. The carcasses of western lesser spot-nosed monkeys were observed being stored and shipped from seaports to be sold at urban hubs (Bissau and Bubaque Island). The effect of commercial trade on the species could be severe, considering the small, naturally occurring, carrying capacities typical of insular ecosystems. The results of this study highlight the importance of understanding the leading social drivers of wild meat hunting of lesser spot-nosed monkeys on the Bijagós Archipelago, and the need to conduct baseline research on these insular populations, for which qualitative and quantitative methods could be combined.

Non-threatened primates are often overlooked in conservation efforts despite their increasing vulnerability to local extirpation. Campbell’s ( Cercopithecus campbelli ) and green monkeys ( Chlorocebus sabaeus ) are sympatric medium-sized West African guenons (tribe Cercopithecini) whose intraspecific genetic diversity remains understudied in most of their distribution. Both species are ecological generalists and are globally considered non-threatened. In Guinea–Bissau, C. campbelli and Chl. sabaeus are considered the most abundant of the ten extant primate species and are the most frequently hunted for meat. Their populations are thought to be decreasing and but up-to-date data on their occurrence in the country hinders their conservation status assessment. We aimed to update occurrence data and estimate the country-wide mitochondrial (mtDNA) genetic diversity for both species in Guinea–Bissau. From 2008–2022, we conducted surveys in four mainland protected areas and on the islands of the Bijagós Archipelago. We identified C. campbelli populations outside their known distribution. We found high mtDNA diversity for both species on the mainland and lower diversity in insular populations. Our results show significant signals of geographically induced mtDNA differentiation, particularly in C. campbelli . In Chl. Sabaeus , we found divergent haplotypes at geographically close locations. We identified differentiated haplogroups with an estimated divergence time of 1.53 million years ago (Ma) in C. campbelli and 1.16 Ma in Chl. sabaeus, possibly linked to Pleistocene climatic fluctuations. Given the local presence of differentiated mtDNA haplogroups across these and other primate species, we suggest that Guinea–Bissau should be considered as an important region for primate conservation in West Africa.

Dispersal behavior influences gene flow and the spatial distribution of genetic diversity, which is crucial for a species' evolutionary trajectory and population persistence under environmental changes. We used gene flow as a proxy to investigate dispersal patterns in the grayfoot chacma baboon ( Papio ursinus griseipes ) in Gorongosa National Park (GNP), central Mozambique. The baboons inhabit a mosaic landscape with a seasonally variable environment. Thirty-two years ago, GNP was the epicenter of a major war that severely reduced apex predators, resulting in limited mammalian predation on baboons. We aimed to characterize genetic diversity, examine the extent and direction of sex-biased gene flow at different time frames and investigate changes in population size and recent migration events. We collected 121 non-invasive DNA samples and analyzed uni- and bi-parentally inherited markers, comprising mitochondrial DNA, autosomal and Y-linked microsatellites, at two geographic locations (GNP and Catapú Forest Reserve) 150 km apart. We observed high genetic diversity and no evidence of a recent population decline. We identified six mitochondrial haplotypes, including a genetically distinct one in Catapu Forest Reserve. We found molecular evidence for historical and current male-mediated gene flow and female philopatry. Our results highlight the resilience of dispersal patterns in Papio sp . in diverse and seasonally variable ecosystems which have been disturbed by anthropogenic activities.

The green monkey Chlorocebus sabaeus, L. 1766, native to West Africa, was introduced to the Cabo Verde Archipelago in the 16th century. Historical sources suggest that, due to the importance of Cabo Verde as a commercial entrepôt in the Atlantic slave trade, establishing the precise place of origin of this introduced species is challenging. Non-invasive fecal samples were collected from feral and captive green monkey individuals in Cabo Verde. Two mitochondrial fragments, HVRI and cyt b, were used to confirm the taxonomic identification of the species and to tentatively determine the geographic origin of introduction to the archipelago from the African continent. By comparing the new sequences of this study to previously published ones, it was shown that Cabo Verde individuals have unique haplotypes in the HVRI, while also showing affinities to several populations from north-western coastal Africa in the cyt b, suggesting probable multiple sources of introduction and an undetermined most probable origin. The latter is consistent with historical information, but may also have resulted from solely using mtDNA as a genetic marker and the dispersal characteristics of the species. The limitations of the methodology are discussed and future directions of research are suggested.

Illegal wildlife trade (IWT) is considered one of the largest global illegal industries that negatively impacts biodiversity and sustainable development worldwide. DNA barcoding coupled with high-throughput sequencing has been shown to be useful in identifying taxa affected by IWT and has been routinely used during the last decades. However, for countries lacking laboratory infrastructures and sequencing units or trained staff, the application of DNA barcoding tools in conservation actions and policies is limited and dependent on slow sample export processes and molecular analyses carried out abroad. Guinea-Bissau (GB) is located on the West-African coast and has one of the lowest human development indices worldwide, while being a biodiversity hotspot facing many conservation challenges due to illegal commercial hunting, and trade in bushmeat and live individuals. Here, we explore the potential of using inexpensive and portable miniaturised laboratory equipment (MLE) to i) identify species illegally traded in GB using DNA barcoding methods and ii) to improve molecular biology and conservation genetic education and training in GB. Our overarching aim is to raise awareness of the current gap between the need to apply conservation genetic technologies in GB and the inability to do so due to a lack of laboratory infrastructures, sequencing units and opportunities for molecular biology training. We show that MLE can be a solution to accelerate the use of DNA barcoding methods to understand IWT and to train students, technicians and staff from governmental agencies dedicated to investigating environmental crimes, ultimately advancing the discipline of conservation genetics in the country.

Habitat destruction and bushmeat hunting are promoting world-wide fragmentation and demographic contractions of primate populations, of which insular populations are thought to be particularly susceptible to extinction because of a presumably reduced genetic diversity and evolutionary potential. The Bijagós archipelago (BA), located off the coast of Guinea-Bissau (GB) in West Africa, sustain high levels of biodiversity of worldwide-recognised importance. The primate species occurring at BA – the Western lesser spot-nosed guenon (Cercopithecus petaurista buettikoferi), mona monkey (Cercopithecus campbelli) and, the green monkey (Chlorocebus sabaeus) – are at the fringe of distribution and may have a high conservation value. Insular populations of C. p. buettikoferi are presumably the last populations in GB but have never been genetically surveyed across different islands. In this work, I aimed at updating the occurrence of the three primates species in BA, investigate their most likely mainland origin and evaluate their extinction vulnerability by estimating genetic diversity, population substructure and demographic history. Non-invasive DNA sampling was conducted in seven islands of BA and five different protected areas in the mainland. Fragments of mitochondrial DNA (cytochrome b gene and, mitochondrial control region) and ten autosomal microsatellite loci were used as genetic markers. C. p. buettikoferi’s and C. campbelli‘s occurrence in sampled islands seems to remain unaltered from the most recent but twenty-years-old surveys carried out in BA. However, Chl. sabaeus seems to be currently absent from Galinha, Canhabaque, Uno, Uracane and Caravela. For the primates occurring at both BA and mainland, insular populations were genetically less diverse, particularly C. campbelli. The surrounding areas of the Geba Channel (Quinara administrative region) were suggested as the probable source of insular populations. The genetic diversity of insular C. p. buettikoferiwas not exceedingly low for both genetic markers at sampled islands. The population seems to be strongly structured by island, but evidence for migration between islands and admixture between genetic clusters were found. Naturally occurring gene flow between islands is improbable considering socio-ecological features of the species, and human-induced translocation of individuals may be a more likely explanation. The present work was the most complete genetic assessment of the three guenon species occurring at BA to date. It highlighted the importance of human communities in shaping past and current genetic dynamics of these insular populations by presumably promoting translocations to and within BA while also suggesting that primate populations may be negatively impacted if environmental damaging anthropogenic activities increase in the future.

Effective population size (Ne) is a key concept in evolutionary and conservation biology. The western chimpanzee (Pan troglodytes verus) is a Critically Endangered taxon. In Guinea-Bissau, chimpanzees are mainly threatened by habitat loss, hunting and diseases. Guinea-Bissau is considered a key area for its conservation. Genetic tools have not yet been applied to inform management and no estimates of Ne have been obtained. In this study, we use country’s range-wide microsatellite data and five whole-genome sequences to estimate several Ne and infer the recent and ancient demographic history of populations using different methods. We also aim to integrate the different Ne estimates to improve our understanding of the evolutionary history and current demography of this great ape and to discuss strengths and limitations of each estimator and their complementarity in informing conservation decisions. Results from the PSMC method suggest a large ancestral Ne, likely due to ancient structure over the whole subspecies distribution until approximately 10-15,000 years ago. After that, a change in connectivity, a real decrease in size or a combination of both occurred, which reduced the then still large ancestral population to a smaller size (MSVAR: ∼10,000 decreasing to 1,000-6,000 individuals), possibly indicating a fragmentation into coastal and inner subpopulations. In the most recent past, contemporary Ne is below or close to 500 (GONE: 116-580, NeEstimator: 107-549), suggesting a high risk of extinction. The populations at coastal Parks may have been small or isolated for several generations whereas the Boé Park one exhibit higher long-term Ne estimates and can be considered a stronghold of chimpanzee conservation. Through combining different types of molecular markers and analytical methodologies, we try to overcome the limitations of obtaining high quality DNA sampling from wild threatened populations and estimate Ne at different temporal and spatial scales, which is crucial information to make informed conservation decisions at local and regional scales.