Population biology and genomics of Robusta coffee in the Congo basin

Tropical rainforests cover only 7% of the earth’s surface, but they are by far the richest biomes in terms of vascular plant diversity (Kier et al. 2005; Kreft & Jetz 2007). Tropical rainforests are also crucially important in levelling global climate patterns and they provide numerous ecosystem services (Slik et al. 2015). Yet, in the past decades, logging, hunting and other human activities have resulted in severe biodiversity losses, altered ecosystem functioning and net carbon losses in all major tropical forests (Gardner et al. 2009, Baccini et al. 2017). To ensure the resilience and long-term stability of tropical rainforests, fostering the regeneration of the occurring woody plant species is critical (Norden et al. 2009).

Plant regeneration and fitness depend on multiple processes, including pollination, seed dispersal, germination and seedling establishment (Barrett & Eckert 1990). Crucial aspects of gene flow early in the regeneration cycle, such as pollination and seed dispersal, have become strongly jeopardized through ongoing large-scale anthropogenic disturbances of tropical forests (Neuschulz et al. 2016). Pollination processes in tropical rainforest are particularly vulnerable to disturbances, because canopy trees and many understory shrubs typically occur in population densities of less than one individual per hectare (Hubbell & Foster 1986), while self-fertilization is uncommon due to widespread dioecy and self-incompatibility (SI) (Bawa et al. 1985). Tropical trees and shrubs are thus highly dependent on robust pollinator communities, which may be negatively affected by anthropogenic forest disturbance such as logging and modification of the understory (Campbell et al. 2018). Research on species gene flow and pollinator communities is thus fundamental for the survival of species in tropical rainforests. An excellent model for this type of research is Coffea canephora (Robusta coffee).

C. canephora is a long-lived, SI perennial shrub species native to Central Africa. It currently accounts for about 35% of coffee production worldwide, and its importance is expected to increase because it has a higher disease resistance (e.g. Pohlan 2012) and is probably less susceptible to climate change than Arabica coffee (Coffea arabica) (Craparo et al. 2015; Davis et al. 2012). Like many tropical tree and shrub species, wild C. canephora populations are generally small (a few trees per ha) and disconnected (Musoli et al. 2009; Filip Vandelook pers. obs.). The red fleshy fruits are dispersed by gravity and ingestion through birds and mammals. Whereas bees (Hymenoptera) and two-winged flies (Diptera) are the main pollinators in Robusta plantations (Willmer and Stone 1989; Klein et al. 2003a), very little is known about pollinator species and pollinator specificity of C. canephora in the wild, as is the case for most tropical rainforest understory plants (Bawa 1990).
Domesticated C. canephora has been identified in the oriental part of the Congo basin, Uganda and northern Tanzania long before their colonization by Europeans in the early 1900s (Chevalier 1929; Thomas 1935). From the end of the 19th century, C. canephora was developed as a plantation crop in multiple Central African countries, resulting in transport of genetic material of the species throughout the continent (Thomas 1947).