Occurence data for species distribution modelling of wild Coffea canephora

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.