Degradation and regeneration of tropical forests can strongly affect gene flow in understorey species, resulting in genetic erosion and changes in genetic structure. Yet, these processes remain poorly studied in tropical Africa. Coffea canephora is an economically important species, found in the understorey of tropical rainforests of Central and West Africa, and the genetic diversity harboured in its wild populations is vital for sustainable coffee production worldwide. Here, we aimed to quantify genetic diversity, genetic structure, and pedigree relations in wild C. canephora populations, and we investigated associations between these descriptors and forest disturbance and regeneration. Therefore, we sampled 256 C. canephora individuals within 24 plots across three forest categories in Yangambi (DR Congo), and used genotyping-by-sequencing to identify 18,894 SNPs. Overall, we found high genetic diversity, and no evidence of genetic erosion in C. canephora in disturbed old-growth forest, as compared to undisturbed oldgrowth forest. In addition, an overall heterozygosity excess was found in all populations, which was expected for a selfincompatible species. Genetic structure was mainly a result of isolation-by-distance, reflecting geographical location, with low to moderate relatedness at finer scales. Populations in regrowth forest had lower allelic richness than populations in old-growth forest and were characterised by a lower inter-individual relatedness and a lack of isolation-by-distance, suggesting that they originated from different neighbouring populations and were subject to founder effects. Wild Robusta coffee populations in the study area still harbour high levels of genetic diversity, yet careful monitoring of their response to ongoing forest degradation remains required.

Despite their key role in biodiversity conservation, forests in the Congo Basin are increasingly threatened by human activities, but it remains challenging to assess the impact of forest degradation under a more or less intact canopy. Likewise, forest recovery following agricultural abandonment remains poorly understood in the Congo Basin. Here, we surveyed 125 vegetation quadrats across 25 forest inventory plots in the Yangambi area. We aimed to find associations between both selective logging and forest recovery, and a range of forest community and tree community trait characteristics, as compared to reference undisturbed old-growth forest. We found that plots in undisturbed old-growth forest harboured both more tree individuals and tree species with a higher wood density as compared to plots in disturbed old-growth forest. In addition, their tree community composition was significantly different, whereas species diversity recovered since relatively recent agricultural abandonment (< 60 years), community composition and forest structure remained significantly different from the plots in undisturbed old-growth forest. Our study provides some insights into the rate of forest recovery in the Congo basin after agricultural abandonment and highlights the need of proper conservation of the remaining relatively undisturbed old-growth forests. Finally, we stress the need for more extensive vegetation surveys in the Congo Basin to further unravel the effects of anthropogenic disturbance.

Premise Many cultivated coffee varieties descend from Coffea canephora, commonly known as Robusta coffee. The Congo Basin has a century‐long history of Robusta coffee cultivation and breeding, and is hypothesized to be the region of origin of many of the cultivated Robusta varieties. Since little is known about the genetic composition of C. canephora in this region, we assessed the genetic diversity of wild and cultivated C. canephora shrubs in the Democratic Republic of the Congo. Methods Using 18 microsatellite markers, we studied the genetic composition of wild and backyard‐grown C. canephora shrubs in the Tshopo and Ituri provinces and multiple accessions from the INERA Yangambi Coffee Collection. We assessed genetic clustering patterns, genetic diversity, and genetic differentiation between populations. Results Genetic differentiation was relatively strong between wild and cultivated C. canephora shrubs, and both gene pools harbored multiple unique alleles. Strong genetic differentiation was also observed between wild populations. The level of genetic diversity in wild populations was similar to that of the INERA Yangambi Coffee Collection, but local wild genotypes were mostly missing from that collection. Shrubs grown in the backyards were genetically similar to the breeding material from INERA Yangambi. Conclusions Most C. canephora that is grown in local backyards originated from INERA breeding programs, while a few shrubs were obtained directly from surrounding forests. The INERA Yangambi Coffee Collection could benefit from an enrichment with local wild genotypes to increase the genetic resources available for breeding purposes and to support ex situ conservation.