The assessment of population vulnerability under climate change is crucial for planning conservation as well as for ensuring food security. Coffea canephora is, in its native habitat, an understory tree that is mainly distributed in the lowland rainforests of tropical Africa. Also known as Robusta, its commercial value constitutes a significant revenue for many human populations in tropical countries. Comparing ecological and genomic vulnerabilities within the species’ native range can provide valuable insights about habitat loss and the species’ adaptive potential, allowing to identify genotypes that may be act as a resource for varietal improvement. By applying species distribution models, we assessed ecological vulnerability as the decrease in climatic suitability under future climatic conditions from 492 occurrences. We then quantified genomic vulnerability (or risk of maladaptation) as the allelic composition change required to keep pace with predicted climate change. Genomic vulnerability was estimated from genomic environmental correlations throughout the native range. Suitable habitat was predicted to diminish to half its size by 2050, with populations near coastlines and around the Congo River being the most vulnerable. Whole-genome sequencing revealed 165 candidate SNPs associated to climatic adaptation in C. canephora, which were located in genes involved in plant response to biotic and abiotic stressors. Genomic vulnerability was higher for populations in West Africa and in the region at the border between DRC and Uganda. Despite an overall low correlation between genomic and ecological vulnerability at broad scale, these two components of vulnerability overlap spatially in ways that may become damaging. Genomic vulnerability was estimated to be 23% higher in populations where habitat will be lost in 2050 compared to regions where habitat will remain suitable. These results highlight how ecological and genomic vulnerabilities are relevant when planning on how to cope with climate change regarding an economically important species.

Coffea canephora is a self-incompatible evergreen tree species which likely originates from the sub-equatorial lowland rainforests of Africa (Berthaud, 1986; Davis et al., 2006). The species is distributed in the understory of evergreen and semi-deciduous tropical rainforests of the Guineo-Congolian region (Gomez et al., 2009). Wild populations of C. canephora are found as distant patches of few individuals, generally consisting of the parents and offspring scattered up to a few kilometres (Berthaud, 1986).

Combining all known georeferenced data from seven herbaria and two living collections, we obtained a total of 526 carefully checked occurrence records covering the entire range known for wild C. canephora.