Phylogeography, conservation genetics and parasitology of chimpanzees (Pan troglodytes verus) in Guinea-Bissau, West Africa.
Authors: Sá Rui 
Published: July 2018

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.