Peter Frandsen:
Adaptive Evolution and Demographic History of African Great Apes

Date: 13-08-2016    Supervisor: Hans R. Siegismund & Anders Albrechtsen

With offset in the central theme of adaptive evolution and demographic history of African great apes, the work presented in this thesis entails some of the recent advances in population genomics of our closest living relatives. With a transition from traditional genetics to genome wide sequencing of many individuals from the same species or populations, it has recently become possible to gain novel insight to a range of evolutionary aspects in the great apes with pronounced implication for conservation efforts for these threatened species.

In what is the first population genomic study of the mountain gorilla, we explored the evolutionary consequences of thousands of generations with declining population sizes and severe inbreeding. Our findings showed that present-day populations have the lowest genetic diversity of all great apes. Still they have managed to persist for more than 100,000 years at very low population sizes. The less than 800 remaining individuals are however critically endangered in the wild today and with their low genetic diversity, the mountain gorilla is extremely vulnerable to anthropogenic encroachment on their natural habitat and the associated risk of human transmitted diseases.

From a genome wide study of chimpanzees and bonobos, we show that the demographic history of chimpanzee has involved historic time periods with introgression from bonobos. This is the first robust evidence of gene flow between these two species that diverged for more than one million years ago. With the, to date, most comprehensive analysis of population structure in all four subspecies of chimpanzees, we also find a tight link between genetic diversity and geographical distribution. This has inspired the last chapter of this thesis that attempts to develop a practical genetic tool for global conservation of the chimpanzee. From a panel of ~60 K ancestry informative marker (AIMs), we demonstrate how we can improve ex situ conservation management programmes by accurately assigning subspecies ancestry in chimpanzee breeding populations where this information is most often lost or inaccurate. Furthermore, we show how this panel of AIMs can be used to re-assign geographical origin of chimpanzees that has been confiscated from the illegal trade, providing conservation authorities with a powerful tool to improve conservation efforts for the chimpanzee in the wild.