Phylogeography, conservation genetics and parasitology of chimpanzees (Pan troglodytes verus) in Guinea-Bissau, West Africa.

Abstract

Chimpanzees are disappearing at an alarming rate and it is imperative that strategies should be applied towards their conservation. The evolutionary history of West African chimpanzees remains ambiguous and controversial. Chimpanzees in Guinea-Bissau live at the most western limit of the species distribution and no studies so far have included individuals from this area. Little is known about their ecological, social and behavioural characteristics and their phylogeography and genetic structure has never been evaluated. Furthermore, little is known about their symbiontic fauna.The aims of my Ph.D. research were to evaluate concomitant threat factors that may have a negative impact on chimpanzee persistence in Guinea-Bissau, and to test a set of hypothesis regarding their phylogeographic and genetic structure. First I report on the trade and ethnobiological use of chimpanzee body parts for traditional practices. Second, I investigate how Guinea-Bissau chimpanzees relate to other members of the Pan troglodytes verus subspecies in West Africa especially those from Guinea Conakry in order to uncover their evolutionary history. Third, I assess their genetic diversity and structure where I expected to find significant population genetic structure among isolated subpopulations. Finally, I investigate the gastrointestinal symbiont diversity of chimpanzees living in a disturbed habitat, especially focusing on infection from parasites with direct life cycles and the effects of increased intra and interspecific contact.My research shows that in addition to habitat loss and fragmentation and the pet trade, transnational traffic and the use of chimpanzee body parts for traditional purposes constitute additional threats and must be taken into consideration for conservation measures. Second, I showed that Guinea-Bissau chimpanzees have experienced a complex paleodemographic history revealed by the phylogeographic analyses suggesting that an historical bottleneck followed by several expansion events. Furthermore, a clear pattern of genetic structure was observed where isolation by distance and vicariance have affected patterns of genetic structure. Chimpanzee females were inferred to disperse in a stepping stone way. Moreover, the two main mitochondrial lineages emerged during the early Pleistocene (1-0.78 MYA) and the divergence time of the haplogroups dates back to middle Pleistocene (0.78-0.12 MYA) coincident with the Gunz (0.68-0.62 MYA) and Mindel (0.45-0.30 MYA) glaciations that caused the contraction of west African tropical forests but followed by an expansion afterwards during the interglaciar periods that restored its connectivity. Lastly, I identified at least 13 different symbiotic genera (Troglodytella abrassarti, Troglocorys cava, Blastocystis spp., Entamoeba coli, Iodamoeba buestcshlii, Giardia intestinalis, Chilomastix mesnilii, Bertiella sp., Probstmayria gombensis, unidentified strongylids, Strongyloides stercoralis, Strongyloides fuelleborni and Trichuris sp.), which have colonized the Guinea-Bissau chimpanzee gastrointestinal tract. Symbiont richness was higher in chimpanzee subpopulations living in fragmented forests compared to the community inhabiting continuous forest area. In fragmented areas chimpanzee density and range-use intensity decreased, which might contribute to low prevalence/total absence of Trichuris sp. in samples from chimpanzees in these areas when compared with those inhabiting continuous forest.

First Evidence of Chimpanzee Extractive Tool Use in Cantanhez, Guinea-Bissau: Cross-Community Variation in Honey Dipping

“…Importantly, at both sites tools were used to exploit the same resource, the raw material used was the same (Avicennia germinans), and the hives were exclusively arboreal, located in live trees with small entryways. Hence, the differences in tools cannot easily be explained through environmental differences, and a genetic explanation is unlikely given the documented gene flow between communities (Sá, 2013). Therefore, again a cultural explanation is likely, this time pertaining to subtle differences in the characteristics of tool manufacture and use between the Cambeque and Madina communities.…”

“…It is estimated that there are 10-12 chimpanzee communities in CNP as a whole (Bersacola, 2019). In the forested areas of centralsouthern CNP, genetic, behavioural and ecological research support the presence of seven different chimpanzee communities (Hockings and Sousa, 2013;Sá, 2013;Bessa et al, 2015;Bersacola, 2019;Vieira et al, 2019;Hockings et al, 2020); these include the four studied communities: Caiquene-Cadique, Lautchandé, Madina and Cambeque. Due to the unhabituated nature of these communities, at present little is known about their community sizes and compositions; nonetheless, previous works estimate that the communities' range between 35-60 individuals (Bessa et al, 2015;Vieira et al, 2019).…”

Inter-community behavioural variation confirmed through indirect methods in four neighbouring chimpanzee communities in Cantanhez NP, Guinea-Bissau

“…We identified different communities based on previous research, including genetic studies, local knowledge and the presence of natural and anthropogenic barriers (e.g. villages, roads, rivers and estuary branches that form small peninsulas) [38,39,[43][44][45][46]. The size of each community's ranging area was estimated using minimum convex polygons: Caiquene-Cadique 14. royalsocietypublishing.org/journal/rsos R. Soc.…”